# GBrain — Full Context

> GBrain is a personal knowledge brain and GStack mod for agent platforms. Pluggable engines (PGLite default, Postgres+pgvector for scale), contract-first operations, 26 fat-markdown skills. Teaches agents brain ops, ingestion, enrichment, scheduling, identity, and access control.

This file concatenates core GBrain documentation for single-fetch ingestion.
For the link-only index, see `llms.txt`. Source of truth: https://github.com/garrytan/gbrain.

# Core entry points

## AGENTS.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/AGENTS.md

# Agents working on GBrain

This is your install + operating protocol. Claude Code reads `./CLAUDE.md` automatically.
Everyone else (Codex, Cursor, OpenClaw, Aider, Continue, or an LLM fetching via URL):
start here.

## Install (5 min)

1. Install gbrain via Bun (the canonical path):
   ```bash
   curl -fsSL https://bun.sh/install | bash
   export PATH="$HOME/.bun/bin:$PATH"
   bun install -g github:garrytan/gbrain
   ```
   If `bun install -g` aborts or `gbrain doctor` reports `schema_version: 0`,
   the CLI prints a recovery hint pointing at [#218](https://github.com/garrytan/gbrain/issues/218).
   Run `gbrain apply-migrations --yes` to recover, or fall back to the
   deterministic install: `git clone https://github.com/garrytan/gbrain.git ~/gbrain && cd ~/gbrain && bun install && bun link`.
2. Init the brain: `gbrain init` (defaults to PGLite, zero-config). For 1000+ files or
   multi-machine sync, init suggests Postgres + pgvector via Supabase.
3. **STOP — ask the user about search mode.** `gbrain init` auto-applied a
   default but printed a 9-cell cost matrix (mode × downstream model)
   preceded by `[AGENT]` markers. You MUST relay the matrix to the operator
   and confirm their choice before continuing. Cost spread between corners
   is 25x — silent acceptance is the wrong default. See
   [`./INSTALL_FOR_AGENTS.md`](./INSTALL_FOR_AGENTS.md) Step 3.5 for the
   exact ask-the-user protocol. Same banner fires on `gbrain post-upgrade`
   for existing users (search modes were added in v0.32.3).
4. Read [`./INSTALL_FOR_AGENTS.md`](./INSTALL_FOR_AGENTS.md) for the full 9-step flow
   (API keys, identity, cron, verification).

## Read this order

1. `./AGENTS.md` (this file) — install + operating protocol.
2. [`./CLAUDE.md`](./CLAUDE.md) — architecture reference, key files, trust boundaries,
   test layout.
3. [`./docs/architecture/brains-and-sources.md`](./docs/architecture/brains-and-sources.md)
   — the two-axis mental model (brain = which DB, source = which repo in the DB). Every
   query routes on both axes. Read before writing anything that touches brain ops.
4. [`./skills/conventions/brain-routing.md`](./skills/conventions/brain-routing.md) —
   agent-facing decision table: when to switch brain, when to switch source, how
   cross-brain federation works (latent-space only; the agent decides).
5. [`./skills/RESOLVER.md`](./skills/RESOLVER.md) — skill dispatcher. Read before any task.

## Trust boundary (critical)

GBrain distinguishes **trusted local CLI callers** (`OperationContext.remote = false`,
set by `src/cli.ts`) from **untrusted agent-facing callers** (`remote = true`, set by
`src/mcp/server.ts`). Security-sensitive operations like `file_upload` tighten filesystem
confinement when `remote = true` and default to strict behavior when unset. If you are
writing or reviewing an operation, consult `src/core/operations.ts` for the contract.

## Common tasks

- **Configure:** [`docs/ENGINES.md`](./docs/ENGINES.md),
  [`docs/guides/live-sync.md`](./docs/guides/live-sync.md),
  [`docs/mcp/DEPLOY.md`](./docs/mcp/DEPLOY.md).
- **Debug:** [`docs/GBRAIN_VERIFY.md`](./docs/GBRAIN_VERIFY.md),
  [`docs/guides/minions-fix.md`](./docs/guides/minions-fix.md), `gbrain doctor --fix`.
- **Migrate / upgrade:** `gbrain upgrade` (binary self-update + schema migrations + post-upgrade prompts),
  [`docs/UPGRADING_DOWNSTREAM_AGENTS.md`](./docs/UPGRADING_DOWNSTREAM_AGENTS.md),
  [`skills/migrations/`](./skills/migrations/), `gbrain apply-migrations --yes` (manual schema-only).
- **Eval retrieval changes:** capture is off by default. To benchmark a
  retrieval change against real captured queries, set
  `GBRAIN_CONTRIBUTOR_MODE=1`, then `gbrain eval export --since 7d > base.ndjson`
  and `gbrain eval replay --against base.ndjson`. For public benchmark
  coverage (LongMemEval, ground-truth scoring), `gbrain eval longmemeval
  <dataset.jsonl>` (v0.28.8) runs against an isolated in-memory PGLite
  per question — your `~/.gbrain` is never opened. Full guide:
  [`docs/eval-bench.md`](./docs/eval-bench.md).
- **Drive the brain to a target health score (v0.36.4.0):** the one-command
  loop. `gbrain doctor --remediation-plan --json` previews what would be
  fixed; `gbrain doctor --remediate --yes --target-score 90 --max-usd 5`
  walks a dependency-ordered plan (sync before extract, embed after
  consolidate), re-checking score between every step, refusing to spend
  past the cost cap. Empty brains (no entity pages) or unconfigured embedding
  keys hit a `max_reachable_score` ceiling and bail with what's missing.
  Three phase handlers (synthesize / patterns / consolidate) are
  PROTECTED — only trusted local callers can submit them; MCP cannot.
  Reference: [`docs/architecture/topologies.md`](./docs/architecture/topologies.md)
  and the CHANGELOG entry for v0.36.4.0.
- **Track a founder/company over time (v0.35.7):** when an entity has
  typed metric claims in its `## Facts` fence (`metric: mrr`, `value: 50000`,
  `unit: USD`, `period: monthly` columns), run
  `gbrain eval trajectory <entity-slug>` for the chronological history
  with regressions auto-flagged, or `gbrain founder scorecard <entity-slug>`
  for a four-signal JSON rollup (claim_accuracy / consistency /
  growth_trajectory / red_flags). MCP op `find_trajectory` exposes the
  same data — read scope, visibility-filtered for remote callers. **v0.40.2.0:**
  `gbrain think` now uses this substrate automatically on temporal /
  knowledge_update intent (default ON; flip `think.trajectory_enabled=false`
  to opt out). Migration v82 added `facts.event_type` so non-metric event
  rows (`meeting`, `job_change`, `location_change`) ride through the same
  pipeline; pass `kind: 'event'` or `'all'` to `find_trajectory` to query
  them.
- **Everything else:** [`./llms.txt`](./llms.txt) is the full documentation map.
  [`./llms-full.txt`](./llms-full.txt) is the same map with core docs inlined for
  single-fetch ingestion.

## Before shipping

Easiest path: `bun run ci:local` runs the full CI gate inside Docker (gitleaks,
unit tests with `DATABASE_URL` unset, then all 29 E2E files sequentially against a
fresh pgvector container) and tears down. Use `bun run ci:local:diff` for the
diff-aware subset during fast iteration on a focused branch. Requires Docker
(Docker Desktop / OrbStack / Colima) and `gitleaks` (`brew install gitleaks`).

Manual path: `bun test` plus the E2E lifecycle described in `./CLAUDE.md` (spin
up the test Postgres container, run `bun run test:e2e`, tear it down).

Ship via the `/ship` skill, not by hand.

## Privacy

Never commit real names of people, companies, or funds into public artifacts. See the
Privacy rule in `./CLAUDE.md`. GBrain pages reference real contacts; public docs must
use generic placeholders (`alice-example`, `acme-example`, `fund-a`).

## Forks

If you are a fork, regenerate `llms.txt` + `llms-full.txt` with your own URL base before
publishing: `LLMS_REPO_BASE=https://raw.githubusercontent.com/your-org/your-fork/main bun run build:llms`.

---

## CLAUDE.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/CLAUDE.md

# CLAUDE.md

GBrain is a personal knowledge brain and GStack mod for agent platforms. Pluggable
engines: PGLite (embedded Postgres via WASM, zero-config default) or Postgres + pgvector
+ hybrid search in a managed Supabase instance. `gbrain init` defaults to PGLite;
suggests Supabase for 1000+ files. GStack teaches agents how to code. GBrain teaches
agents everything else: brain ops, signal detection, content ingestion, enrichment,
cron scheduling, reports, identity, and access control.

## Two organizational axes (read this first)

GBrain knowledge is organized along two orthogonal axes. Users AND agents must
understand both, or queries misroute silently.

- **Brain** — WHICH DATABASE. Your personal brain is `host`. You can mount
  additional brains (team-published, each with their own DB and access policy)
  via `gbrain mounts add` (v0.19+). Routing: `--brain`, `GBRAIN_BRAIN_ID`,
  `.gbrain-mount` dotfile.
- **Source** — WHICH REPO INSIDE THE DATABASE. A brain can hold many sources
  (wiki, gstack, openclaw, essays). Slugs scope per source. Routing:
  `--source`, `GBRAIN_SOURCE`, `.gbrain-source` dotfile.

Both axes follow the same 6-tier resolution pattern. Read
`docs/architecture/brains-and-sources.md` for topology diagrams (personal, team
mount, CEO-class with multiple team brains) and
`skills/conventions/brain-routing.md` for the agent-facing decision table.

## Architecture

Contract-first: `src/core/operations.ts` defines ~47 shared operations (v0.29 adds `get_recent_salience`, `find_anomalies`, `get_recent_transcripts`). CLI and MCP
server are both generated from this single source. Engine factory (`src/core/engine-factory.ts`)
dynamically imports the configured engine (`'pglite'` or `'postgres'`). Skills are fat
markdown files (tool-agnostic, work with both CLI and plugin contexts).

**Trust boundary:** `OperationContext.remote` distinguishes trusted local CLI callers
(`remote: false` set by `src/cli.ts`) from untrusted agent-facing callers
(`remote: true` set by `src/mcp/server.ts`). Security-sensitive operations like
`file_upload` tighten filesystem confinement when `remote=true` and default to
strict behavior when unset.

## Key files

- `src/core/operations.ts` — Contract-first operation definitions (the foundation). Also exports upload validators: `validateUploadPath`, `validatePageSlug`, `validateFilename`, plus `matchesSlugAllowList(slug, prefixes)` (v0.23 glob matcher: `<prefix>/*` matches recursive children; bare `<prefix>` matches exact only). `OperationContext.remote` flags untrusted callers; `OperationContext.allowedSlugPrefixes` (v0.23) is the trusted-workspace allow-list set by the dream cycle. `put_page` enforces: when `viaSubagent` and `allowedSlugPrefixes` is set, slug must match the allow-list; else the legacy `wiki/agents/<id>/...` namespace check applies. Auto-link enabled for trusted-workspace writes (skipped only when `remote=true && !trustedWorkspace`). As of v0.26.0, every `Operation` also carries `scope?: 'read' | 'write' | 'admin'` + `localOnly?: boolean`. All ops are annotated; `sync_brain`, `file_upload`, `file_list`, and `file_url` are `admin + localOnly` (rejected over HTTP). `OperationContext.auth?: AuthInfo` is threaded through HTTP dispatch for scope enforcement in `serve-http.ts` before the op runs. **v0.26.9 (D12 + F7b):** `OperationContext.remote` is now a REQUIRED field in the TypeScript type — the compiler is the first defense against transports that forget to set it. Four trust-boundary call sites (`put_page` allowlist, file_upload trust-narrowing, submit_job protected-name guard, auto-link skip) flipped from falsy-default (`!ctx.remote`) to fail-closed semantics (`ctx.remote === false` for "trusted-only" sites and `ctx.remote !== false` for "untrust unless explicit-false"). Anything that isn't strictly `false` is now treated as remote. Closed an HTTP MCP shell-job RCE: a `read+write`-scoped OAuth token could submit `shell` jobs because the HTTP request handler's literal context skipped `remote: true` and `submit_job`'s protected-name guard saw a falsy undefined. Stdio MCP set the field correctly via dispatch.ts; HTTP inlined a parallel context-builder for several releases and lost it. **v0.34.1.0 (#861 + #876):** new helper `sourceScopeOpts(ctx)` encodes the precedence ladder for source-scoped reads — federated array (`ctx.auth.allowedSources`) wins over scalar (`ctx.sourceId` / `ctx.auth.sourceId`) over nothing. Every read-side op handler routes through it so future ops can't silently drift from the canonical v0.31.8 thread. Closes the source-isolation leak on the read path: a `read+write`-scoped OAuth client bound to `--source dept-x` no longer sees rows from neighboring sources via `search` / `query` / `list_pages` / `get_page` / `find_experts` / `query`'s image path. **v0.41.30.0:** `put_page`'s v0.38 inline disk write-through (the bare `writeFileSync` into `sync.repo_path`) extracted into the shared `writePageThrough` helper (`src/core/write-through.ts`) that `put_page` now calls — behavior preserved (same render-from-row + frontmatter-override stamping) and upgraded to ATOMIC (temp-sibling + rename), so a crash or concurrent `gbrain sync` can no longer read a half-written `.md`. The same helper now also backs `gbrain brainstorm/lsd --save`.
- `src/core/engine.ts` — Pluggable engine interface (BrainEngine). `clampSearchLimit(limit, default, cap)` takes an explicit cap so per-operation caps can be tighter than `MAX_SEARCH_LIMIT`. Exports `LinkBatchInput` / `TimelineBatchInput` for the v0.12.1 bulk-insert API (`addLinksBatch` / `addTimelineEntriesBatch`). As of v0.13.1, `BrainEngine` has a `readonly kind: 'postgres' | 'pglite'` discriminator so migrations (`src/core/migrate.ts`) and other consumers can branch on engine without `instanceof` + dynamic imports. **v0.29:** four new methods — `batchLoadEmotionalInputs(slugs?)` (CTE-shaped read with per-table aggregates so a page × N tags × M takes never produces N×M rows), `setEmotionalWeightBatch(rows)` (`UPDATE FROM unnest($1::text[], $2::text[], $3::real[])` composite-keyed on `(slug, source_id)` for multi-source safety), `getRecentSalience(opts)`, `findAnomalies(opts)`. `PageFilters` extended with `sort?: 'updated_desc' | 'updated_asc' | 'created_desc' | 'slug'` + `PAGE_SORT_SQL` whitelist consumed by both engines (was hardcoded `ORDER BY updated_at DESC`). **v0.32.8 (PR #860):** new `listAllPageRefs(): Promise<Array<{slug, source_id}>>` ordered by `(source_id, slug)`. Cheap cross-source enumeration for hot loops on large brains — replaces the `getAllSlugs()→getPage(slug)` N+1 pattern in extract-takes, extract, integrity, which silently defaulted to `source_id='default'` for non-default-source pages. Implementation parity across postgres-engine.ts + pglite-engine.ts. Pinned by `test/e2e/multi-source-bug-class.test.ts`. **v0.34.1.0 (#861):** `SearchOpts` + `PageFilters` add `sourceIds?: string[]` for the federated read axis; both engines apply `WHERE source_id = ANY($N::text[])` when the array is set and preserve the scalar `sourceId` fast path when unset. `traverseGraph(slug, depth, opts?)` and `traversePaths(slug, opts?)` accept `opts.sourceId` / `opts.sourceIds` so graph walks respect the caller's scope. **T8 wave (pgGraph-inspired CI infra, v0.37.4.0):** `traverseGraph` opts gains `frontierCap?: number` (per-iteration cap on the recursive CTE — approximately per-BFS-layer). Return type stays `Promise<GraphNode[]>` for MCP wire stability. New export `TraverseGraphOpts`. Postgres path uses parenthesized `LIMIT N ORDER BY (slug, id)` inside the recursive term; PGLite mirrors with positional params + the same shape SQL. Pinned by `test/regressions/v0_36_frontier_cap.test.ts` (4 contracts: cap-unset back-compat, cap-hit bounds result to `<= cap+1`, MCP wire-shape preservation, concurrency independence). **`onTruncation` callback designed but stripped pre-merge in /review** — adversarial pass caught false-positive (organic count == cap) + false-negative (LIMIT-before-DISTINCT in diamond graphs) cases in the v1 algorithm. Restoring the signal requires a dedupe-then-cap SQL rewrite + Postgres parity E2E — see TODOS.md → "T8 truncation signal". **v0.35.6.0:** two new methods supporting the phantom-redirect cycle pass — `refreshPageBody(slug, sourceId, compiled_truth, timeline, content_hash)` narrow-UPDATEs three columns + updated_at, skipping soft-deleted rows (codex #7: content_hash refresh is required so `gbrain sync` sees the canonical as unchanged after fence merge); `migrateFactsToCanonical(phantomSlug, canonicalSlug, sourceId)` UPDATEs `entity_slug` + `source_markdown_slug` on every active fact row keyed on the phantom, preserving embedding/validUntil/kind/status/source_session/confidence — codex #3 fix for the writeFactsToFence lossy-migration trap. Both methods have engine parity tests at `test/phantom-redirect-engine-parity.test.ts`. **v0.40.4.0:** new `getAdjacencyBoosts(pageIds): Promise<Map<number, AdjacencyRow>>` method powers the per-query graph-signals stage in hybrid search. Single SQL query returns inbound-link counts among the top-K set plus a cross-source count (links from pages whose `source_id` differs from the target's). `COALESCE(p.source_id, 'default')` for null safety; `HAVING >= 1` matches JSDoc; cross-source CASE-WHEN on the JOINed target row excludes the target's own source. Parity SQL between postgres-engine.ts + pglite-engine.ts. `SearchResult` gains 12 new optional fields (`base_score`, `backlink_boost`, `salience_boost`, `recency_boost`, `exact_match_boost`, `graph_adjacency_boost`, `graph_cross_source_boost`, `session_demote_factor`, `reranker_delta`, plus internal staging fields). Pinned by `test/e2e/graph-signals-engine.test.ts` (7 cases) + cross-engine parity in the same suite. **v0.41.25.0 (supersedes PR #1538):** two new REQUIRED methods on BrainEngine — `deletePages(slugs, {sourceId}): Promise<string[]>` (single-batch primitive returning slugs actually deleted, D6) and `resolveSlugsByPaths(paths, {sourceId}): Promise<Map<path,slug>>` (batch path→slug lookup). `sourceId` is REQUIRED on both at the type level (D5; asymmetric with single-row `deletePage` which keeps optional/'default' fallback — v0.42+ TODO to tighten). Both methods short-circuit on empty input and throw when called with `> DELETE_BATCH_SIZE`. Closes the 73K-delete-jams-sync bottleneck for both engines. **v0.41.31.0 (stale-embedding-semantics wave):** four engine-interface changes for real model/dims-swap stale detection. (1) `countStaleChunks(opts?)` gains an optional `signature?: string` — when set, the stale predicate widens from `embedding IS NULL` to ALSO include chunks whose JOINed page `embedding_signature IS NOT NULL AND <> $signature` (a model/dims swap). NULL signature is GRANDFATHERED (never counted) so the post-migration-v108 corpus isn't flagged en masse; omit `signature` for the legacy NULL-only count. (2) New `sumStaleChunkChars(opts?: {sourceId?, signature?}): Promise<number>` — `SUM(LENGTH(chunk_text))` over stale chunks (same stale predicate + embed_skip filter + optional sourceId scope as `countStaleChunks`); used by the `gbrain sync --all` cost preview to price the embedding backlog via `estimateCostFromChars`. (3) New `setPageEmbeddingSignature(slug, {sourceId?, signature})` — stamps `pages.embedding_signature` for one page after its chunks are (re)embedded; idempotent, no-op when the page doesn't exist. (4) New `invalidateStaleSignatureEmbeddings({signature, sourceId?}): Promise<number>` — NULLs `embedding` + `embedded_at` on every chunk whose page `embedding_signature` is set AND differs from `signature`, returns the count invalidated; the embed-stale loop calls it BEFORE `listStaleChunks` so signature-drift pages flow through the existing NULL-embedding keyset cursor unchanged (GRANDFATHER: NULL signature never invalidated). Implementation parity across postgres-engine.ts + pglite-engine.ts. Also widens `findOrphanPages(opts?: {sourceId?, sourceIds?})` per the v0.41.29.0 orphan-source-scoping wave (candidate-side scoping only; inbound links counted from any source). Pinned by `test/sum-stale-chunk-chars.test.ts`, `test/embedding-signature-stale.test.ts`, `test/e2e/engine-parity.test.ts`. **v0.41.34.0 (retrieval-maxpool incident, T3):** two new methods for the free-text alias layer — `resolveAliases(aliasNorms, opts?): Promise<Map<string, Array<{slug, source_id}>>>` (READ side; maps each normalized alias to the `(slug, source_id)` pairs that declare it, source-scoped via `sourceId`/`sourceIds`) and `setPageAliases(slug, sourceId, aliasNorms)` (WRITE side; replaces the full alias set for one `(slug, source)` — delete then insert, empty clears, idempotent on the unique triple). Called by the ingest projection in `importFromContent` and the `reindex --aliases` backfill so a page's declared aliases stay in lockstep with its frontmatter. Implementation parity across both engines; pinned by `test/search/page-aliases-engine.test.ts`. `searchVector` in both engines now injects the shared `buildBestPerPagePoolCte` per-page max-pool (T1) so a page surfaces on its strongest chunk, not whichever single chunk won the inner LIMIT.
- `src/core/engine-constants.ts` (v0.41.25.0, NEW) — single source of truth for engine batch-sizing constants. Exports `DELETE_BATCH_SIZE = 500` consumed by both engines' `deletePages` + `resolveSlugsByPaths` and by the sync delete + rename loops. Lives outside `engine.ts` (the interface module) to avoid circular-import worry. Same order-of-magnitude as `addLinksBatch`'s effective per-call budget — bounded per-statement work for predictable lock hold time + write amplification.
- `src/core/search/graph-signals.ts` (v0.40.4.0) — per-query graph-signals helper. `applyGraphSignals(results, engine, opts)` runs as the 4th post-fusion stage (after backlink/salience/recency). Three boosts: `ADJACENCY_BOOST=1.05` (page is linked from 2+ OTHER top-K results — local hub for THIS query), `CROSS_SOURCE_BOOST=1.10` (page is linked from 2+ DIFFERENT sources — corroborated across team brains, dormant in single-source brains), `SESSION_DEMOTE=0.95` (3+ results from same chat session — keep the highest-scoring one at full score, demote the rest). All three inherit the v0.35.6.0 floor-ratio gate that prevents weak pages from getting boosted past strong ones via popularity. `computeScoreDistribution(results)` emits min/p25/p50/p75/p95/max + `reorder_band_width` — instrumentation for the v0.41+ magnitude calibration wave (TODOS T-todo-2). `sessionPrefix(slug)` extracts the chat-session anchor (`chat/2026-05-15-...`). Pure `pairedBootstrapPValue(deltas, resamples, rng)` exported for eval gates. Test seam via `adjacencyFn` DI. Fail-open: any error logs via `logGraphSignalsFailure` (JSONL audit via `audit-writer`) and returns the input array unchanged. Pinned by `test/search/graph-signals.test.ts` (24 cases including the IRON-RULE floor-gate regression).
- `src/core/search/hybrid.ts` extension (v0.40.4.0) — `runPostFusionStages` extended with a 4th stage (`graphSignalsEnabled`, `onGraphMeta`, `onScoreDistribution`). `base_score` stamped at function entry idempotently (captured ONCE before any boost stage mutates `score`). Every existing post-fusion stage now stamps its multiplier on the result: `applyBacklinkBoost` → `backlink_boost`, `applySalienceBoost` → `salience_boost`, `applyRecencyBoost` → `recency_boost`. `applyReranker` (called earlier in the pipeline) stamps `reranker_delta` as a rank delta (positive = improved). `applyExactMatchBoost` in `src/core/search/intent-weights.ts` stamps `exact_match_boost` when fired. Per-stage attribution is the cathedral that powers `gbrain search --explain` — every boost surface carries its own field, so `formatResultsExplain` reads them all without coupling to internal stage ordering.
- `src/core/search/explain-formatter.ts` (v0.40.4.0) — renders `SearchResult[]` as a multi-line per-result breakdown for `gbrain search --explain`. Reads every boost-stamping field. Handles the "no boosts applied" empty path. 4-decimal precision with trailing-zero strip. Pinned by `test/search/explain-formatter.test.ts` (19 cases).
- `src/core/search/mode.ts` extension (v0.40.4.0) — new `graph_signals: boolean` knob in `ModeBundle`. Defaults: `conservative=false`, `balanced=true`, `tokenmax=true`. `KNOBS_HASH_VERSION` bumps 3→4 with a `gs=` parts entry appended per the CDX2-F13 cache-key contamination convention so a graph-on cache write can't be served to a graph-off lookup. `SearchKeyOverrides` + `SearchPerCallOpts` + `loadOverridesFromConfig` + `SEARCH_MODE_CONFIG_KEYS` + `resolveSearchMode` + `attributeKnob` all carry the new field. Opt-out per-brain: `gbrain config set search.graph_signals false`. Mid-deploy: existing `query_cache` rows from before the upgrade hash differently — natural row segregation, clears within `cache.ttl_seconds` (3600s default).
- `src/core/audit/audit-writer.ts` (v0.40.4.0, NEW) — shared JSONL audit primitive consolidating the 5 hand-rolled audit modules. Exports `createAuditWriter({kind, recordSchema})` returning `{log, readRecent}` plus shared helpers `computeIsoWeekFilename(kind, now?)` and `resolveAuditDir()` (honors `GBRAIN_AUDIT_DIR`). ISO-week file rotation; best-effort writes (stderr warn on failure, never throws); read-path scans current-week + previous-week files for boundary spans. Five existing audits refactored onto it for parity: `src/core/rerank-audit.ts`, `src/core/audit-slug-fallback.ts`, `src/core/minions/handlers/shell-audit.ts`, `src/core/minions/handlers/supervisor-audit.ts`, `src/core/facts/phantom-audit.ts`. Public API of each module preserved bit-for-bit — every existing test passes unchanged. The new `graph-signals-failures` audit (`logGraphSignalsFailure`) uses the same primitive. Codex F16 (TODOS) calls out one remaining hand-rolled audit at `src/core/skillpack/audit.ts` for a v0.41+ refactor. Pinned by `test/audit/audit-writer.test.ts` (22 cases pinning the contract).
- `src/core/cli-options.ts` extension (v0.40.4.0) — `CliOptions` gains `explain: boolean`. `parseGlobalFlags` recognizes `--explain` anywhere in argv (stripped before command dispatch). `src/cli.ts` `formatResult` for `search` + `query` cases routes to `formatResultsExplain` from `src/core/search/explain-formatter.ts` when `CliOptions.explain` is set; falls through to the existing JSON / human formatters otherwise.
- `src/commands/search.ts:gbrain search stats` extension (v0.40.4.0) — new `graph_signals` section (enabled/source/failures_count/failures_by_reason). JSON envelope adds a `graph_signals` sibling property to existing stats; `_meta.metric_glossary` adds two new keys (`graph_signals.enabled`, `graph_signals.failures_by_reason`). Human output prints the section after the existing block. Reads `search.graph_signals` config first, falls back to the mode default. Pinned by `test/search/search-stats-graph-signals.test.ts` (6 cases).
- `src/commands/doctor.ts` extension (v0.40.4.0) — new `graph_signals_coverage` check wired into both `runDoctor` (local) and `doctorReportRemote` (HTTP/JSON thin-client path). Reads `search.graph_signals` config first, falls back to mode default; silent `ok` when disabled. Computes inbound link coverage on the page set; warns at <10% with `gbrain extract all` fix hint; `ok` at ≥30% ("fire on most queries") and 10-29% ("fire occasionally"), each with the percentage embedded in the message. Pinned by 7 new cases in `test/doctor.test.ts`.
- `src/core/engine-factory.ts` — Engine factory with dynamic imports (`'pglite'` | `'postgres'`)
- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders. As of v0.13.1, `connect()` wraps `PGlite.create()` in a try/catch that emits an actionable error naming the macOS 26.3 WASM bug (#223) and pointing at `gbrain doctor`; the lock is released on failure so the next process can retry cleanly. v0.22.0: `searchKeyword` and `searchKeywordChunks` multiply `ts_rank` by the source-factor CASE expression at the chunk-grain level; `searchVector` becomes a two-stage CTE — inner CTE keeps `ORDER BY cc.embedding <=> vec` so HNSW stays usable, outer SELECT re-ranks by `raw_score * source_factor`. Inner LIMIT scales with offset to preserve pagination contract. As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL — probes for the specific forward-referenced state the embedded schema blob needs (`pages.source_id`, `links.link_source`, `links.origin_page_id`, `content_chunks.symbol_name`, `content_chunks.language`, `sources` FK target table) and adds only what's missing. Closes the upgrade-wedge bug class that bit users 10+ times across 6 schema versions over 2 years (#239/#243/#266/#357/#366/#374/#375/#378/#395/#396). No-op on fresh installs and modern brains. **v0.35.5.0:** probe set extended in parity with postgres-engine.ts — `files.source_id`, `files.page_id`, `oauth_clients.source_id`, `oauth_clients.federated_read`, `sources.archived`, `sources.archived_at`, `sources.archive_expires_at`. Bootstrap also threads the DDL connection from `initSchema` so probes run inside the advisory-lock scope. Closes #1018, #974, #820. **v0.37.10.0:** `getBrainScore` now returns 100/100 with full breakdown components (35/25/15/15/10) when `pageCount === 0`. Vacuous truth — an empty brain has no coverage problem to penalize. Pre-fix, fresh `gbrain init --pglite` users saw "Brain score 0/100" on first `gbrain doctor` run, which was structurally surprising AND triggered the v0.37.8.0 `doctor-report-remote.test.ts` flake (test expected `health_score >= 70` on a freshly-initialized test brain). Mirrored in postgres-engine.ts. Pinned by `test/brain-score-breakdown.test.ts`'s updated empty-brain assertion and the hermetic `test/doctor-report-remote.serial.test.ts`. **v0.41.8.0 (#1247/#1269/#1290/#1340):** two changes. (1) `disconnect()` rewritten with the snapshot+early-null pattern — snapshot `_db`/`_lock` refs and null the instance fields BEFORE any `await` so a concurrent `connect()` cannot observe a partial mid-close state — wrapped in a `try/finally` that guarantees lock-release even if `db.close()` throws (Codex eng-review finding #7 lock-leak guard). KEEPS the original close-then-release order; PR #1337's swap to release-then-close was explicitly rejected because it would widen the window where a sibling process could connect to a still-closing brain. Pinned by `test/pglite-engine-disconnect.serial.test.ts` (5 cases: ordering, snapshot, lock-leak-on-throw, double-disconnect idempotency, reconnect-after-disconnect). (2) New exported `classifyPgliteInitError(message): 'bunfs' | 'macos-26-3' | 'unknown'` + `buildPgliteInitErrorMessage(verdict, original)` route the `PGlite.create()` catch-block hint by failure shape. The `bunfs` verdict matches the literal `$$bunfs` marker OR `ENOENT[\s\S]*pglite\.data` co-occurrence (tightened from a generic `pglite.data` substring per Codex eng-review finding #9); it surfaces a paste-ready `bun upgrade` hint + Node fallback. The `macos-26-3` verdict keeps the existing #223 link. `unknown` falls through to the prior generic hint. Closes the user-facing half of #1340 — pre-fix every `PGlite.create()` failure pointed at #223 regardless of root cause. Pinned by `test/pglite-init-classifier.test.ts` (12 cases including the #1340 reporter's exact error string round-trip). **v0.41.25.0 (supersedes PR #1538):** implements `deletePages(slugs, {sourceId})` + `resolveSlugsByPaths(paths, {sourceId})` via `slug = ANY($1::text[])` array-param binding (the same idiom `addLinksBatch` already uses). Caller-chunking primitive — throws when input exceeds `DELETE_BATCH_SIZE`. Returns `RETURNING slug` rows for `deletePages` so callers can filter `pagesAffected` to confirmed deletes only. **v0.41.31.0:** implements the embedding-signature stale-detection quartet — `sumStaleChunkChars({sourceId?, signature?})`, `setPageEmbeddingSignature(slug, {sourceId?, signature})`, `invalidateStaleSignatureEmbeddings({signature, sourceId?})`, and the widened `countStaleChunks({sourceId?, signature?})`. The `signature` opt widens the stale predicate via `JOIN pages p ... WHERE cc.embedding IS NULL OR (p.embedding_signature IS NOT NULL AND p.embedding_signature <> $signature)` (NULL grandfathered). Parity SQL with postgres-engine.ts. — PGLite-specific DDL (pgvector, pg_trgm, triggers)
- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap. As of v0.12.3, `searchKeyword` / `searchVector` scope `statement_timeout` via `sql.begin` + `SET LOCAL` so the GUC dies with the transaction instead of leaking across the pooled postgres.js connection (contributed by @garagon). `getEmbeddingsByChunkIds` uses `tryParseEmbedding` so one corrupt row skips+warns instead of killing the query. v0.22.0: `searchKeyword`, `searchKeywordChunks`, and `searchVector` apply source-aware ranking by inlining the source-factor CASE and `NOT (col LIKE …)` hard-exclude clause from `src/core/search/sql-ranking.ts`. `searchVector` switches to a two-stage CTE (HNSW-safe inner ORDER BY, source-boost re-rank in the outer SELECT) and carries `p.source_id` through inner→outer for v0.18 multi-source callers. v0.22.1 (#406): `_savedConfig` retains the connect config; `reconnect()` tears down + recreates the pool from saved config (called by supervisor watchdog after 3 consecutive health-check failures). `executeRaw` is a single-statement passthrough — no per-call retry (D3 dropped that as unsound for non-idempotent statements; recovery is supervisor-driven). v0.22.1 (#363, contributed by @orendi84): `connect()` applies `resolveSessionTimeouts()` from `db.ts` as connection-time startup parameters (`statement_timeout`, `idle_in_transaction_session_timeout`) so orphan pgbouncer backends can't hold locks for hours. v0.22.1 (#409, contributed by @atrevino47): `countStaleChunks()` + `listStaleChunks()` server-side-filter on `embedding IS NULL` for `embed --stale`, eliminating ~76 MB/call client-side pull on a fully-embedded brain; `upsertChunks()` resets both `embedding` AND `embedded_at` to NULL when chunk_text changes without a new embedding (consistency). As of v0.22.6.1, `initSchema()` calls `applyForwardReferenceBootstrap()` BEFORE replaying SCHEMA_SQL on the same forward-reference probe set as the PGLite engine, so old Postgres brains pinned at v0.13/v0.18/v0.19 walk forward cleanly instead of wedging on `column "..." does not exist`. **v0.35.5.0:** probe set extended for the column-only forward-reference cases the original v0.22.6.1 sweep missed — `files.source_id`, `files.page_id` (pre-v0.18 brains where `idx_files_source_id` was the choke point), `oauth_clients.source_id`, `oauth_clients.federated_read` (pre-v0.34 brains where v60+v61+v65 chain failed), and `sources.archived` + `sources.archived_at` + `sources.archive_expires_at` (pre-v0.26.5 brains where `CREATE TABLE IF NOT EXISTS sources` was a no-op on existing tables so the archive lifecycle columns never landed). Also (Codex P1 from pre-landing review): the entire probe path now runs on the DDL connection threaded down from `initSchema` — previously probes ran through the instance pool while the advisory lock sat on a different connection, opening a concurrent-bootstrap race for Supabase pooler users. Closes #1018, #974, #820. **v0.28.1:** `disconnect()` is now idempotent. New `_connectionStyle` instance field tracks whether the engine owns its pool (worker engines) or shares the module-level singleton; second call on an instance-pool engine is a no-op rather than falling through to `db.disconnect()` and clobbering the singleton. Pinned by `test/e2e/postgres-engine-disconnect-idempotency.test.ts` (2 cases). Closes the bug class where any test sharing an engine across multiple `worker.start()` / `worker.stop()` cycles silently broke its own DB connectivity. **v0.37.10.0:** `getBrainScore` empty-brain parity with PGLite — returns 100/100 with breakdown components 35/25/15/15/10 when `pageCount === 0` instead of the pre-fix 0/100. Same vacuous-truth rationale as the PGLite side; both engines must agree to keep `doctor-report-remote.serial.test.ts` deterministic. **v0.41.25.0 (supersedes PR #1538):** implements `deletePages(slugs, {sourceId}): Promise<string[]>` via `DELETE FROM pages WHERE slug = ANY($1::text[]) AND source_id = $2 RETURNING slug` (single SQL round-trip per call; caller chunks). Pair `resolveSlugsByPaths` does the `SELECT slug, source_path FROM pages WHERE source_path = ANY($1::text[]) AND source_id = $2` batch lookup. FK cascades through `content_chunks`/`links`/`tags`/`raw_data`/`timeline_entries`/`page_versions`; `files.page_id` + `links.origin_page_id` go SET NULL. Pair primitive throws when input exceeds `DELETE_BATCH_SIZE` (from `src/core/engine-constants.ts`); both methods short-circuit on empty input. **v0.41.31.0:** implements the embedding-signature stale-detection quartet in parity with pglite-engine.ts — `sumStaleChunkChars`, `setPageEmbeddingSignature`, `invalidateStaleSignatureEmbeddings`, and the widened `countStaleChunks` (all accept the optional `signature` to extend "stale" to model/dims-swap drift via the `pages.embedding_signature` JOIN; NULL signature grandfathered). The v0.22.1 `countStaleChunks` / `listStaleChunks` server-side `embedding IS NULL` filter is preserved as the no-signature fast path. Pinned by `test/e2e/engine-parity.test.ts`.
- `src/core/cjk.ts` (v0.32.7 CJK wave) — Single source of truth for CJK detection across the codebase. Exports `CJK_RANGES_REGEX`, `CJK_SLUG_CHARS` (character-class fragment for embedding inside other regexes), `CJK_SENTENCE_DELIMITERS` (`。！？`), `CJK_CLAUSE_DELIMITERS` (`；：，、`), `CJK_DENSITY_THRESHOLD = 0.30`, `hasCJK(s)`, `countCJKAwareWords(s)` (30% density threshold — English docs with one Japanese term stay whitespace-tokenized; Chinese-dominant docs get char-counted), and `escapeLikePattern(s)` (escapes `%`, `_`, `\\` for `ILIKE ... ESCAPE '\\'`). Replaces the inline hasCJK regex previously duplicated at `expansion.ts:58`. BMP-only ranges (Han / Hiragana / Katakana / Hangul Syllables); widening to Unicode property escapes is a v0.33+ TODO. Consumers: `expansion.ts`, `sync.ts:slugifySegment`, `operations.ts:validatePageSlug + validateFilename`, `chunkers/recursive.ts:countWords + DELIMITERS`, `pglite-engine.ts:searchKeyword + searchKeywordChunks`.
- `src/core/audit-slug-fallback.ts` (v0.32.7 CJK wave) — Weekly ISO-week-rotated audit JSONL at `~/.gbrain/audit/slug-fallback-YYYY-Www.jsonl`. `logSlugFallback(slug, sourcePath)` fires when `importFromFile` falls back to a frontmatter slug because `slugifyPath` returned empty (emoji / Thai / Arabic / non-CJK exotic-script filenames). `readRecentSlugFallbacks(days)` reads the last N days for `gbrain doctor`'s `slug_fallback_audit` check. Honors `GBRAIN_AUDIT_DIR` via the shared `resolveAuditDir()` from shell-audit.ts. Separate surface from `sync-failures.jsonl` per codex outside-voice review — that file carries bookmark-gating semantics that info events shouldn't trigger.
- `src/core/embedding-pricing.ts` (v0.32.7 CJK wave) — `EMBEDDING_PRICING` map keyed `provider:model` for the post-upgrade reindex cost estimate. Sibling to `anthropic-pricing.ts`. Entries: OpenAI text-embedding-3-large ($0.13/1M), 3-small ($0.02/1M), ada-002 ($0.10/1M), Voyage 3-large ($0.18/1M), 3 ($0.06/1M). `lookupEmbeddingPrice(modelString)` returns a tagged union (`known` with price + `unknown` with provider name); `estimateCostFromChars(charCount, pricePerMTok)` uses 3.5 chars/token approximation. Unknown providers degrade gracefully to "estimate unavailable" instead of fabricating numbers.
- `src/core/post-upgrade-reembed.ts` (v0.32.7 CJK wave) — Pure functions backing the `gbrain upgrade` chunker-bump cost prompt. `computeReembedEstimate(engine, model)` queries real SQL (`COUNT(*)` + `COALESCE(SUM(LENGTH(compiled_truth)) + SUM(LENGTH(timeline)), 0)`) on `pages WHERE chunker_version < MARKDOWN_CHUNKER_VERSION`. `formatReembedPrompt(est, graceSeconds)` is the stderr-line formatter. `runPostUpgradeReembedPrompt(engine, model, opts)` orchestrates the 10-second Ctrl-C window; TTY-only wait (non-TTY auto-proceeds for CI / cron); `GBRAIN_NO_REEMBED=1` bails out with a doctor-warning marker; `GBRAIN_REEMBED_GRACE_SECONDS=0` skips the wait.
- `src/commands/reindex.ts` (v0.32.7 CJK wave) — `gbrain reindex --markdown [--limit N] [--dry-run] [--json] [--no-embed] [--repo PATH]`. Walks `pages WHERE page_kind = 'markdown' AND chunker_version < MARKDOWN_CHUNKER_VERSION` in 100-row batches, ordered by id. Rows with non-null `source_path` re-import via `importFromFile`; rows without fall back to `importFromContent` against the stored `compiled_truth`. **Both paths pass `forceRechunk: true`** to bypass `importFromContent`'s `content_hash` short-circuit — without that flag (codex post-merge F1), the chunker version bump never reaches pages whose source content hasn't changed since last sync, AND master's v0.32.2 stripFactsFence privacy strip never applies to pre-strip chunks. Idempotent — partial-completion re-runs pick up where they left off via id-ordered batches. Wired into `src/commands/upgrade.ts:runPostUpgrade` after `apply-migrations`. **v0.41.37.0 (#1621):** the DB-only fallback (no source file on disk) no longer passes body-only `compiled_truth` to `importFromContent` — that path re-parsed with EMPTY frontmatter and OVERWROTE the page's real frontmatter / title / timeline (codex catch). It now `getPage` + `getTags`, reconstructs the FULL markdown via `serializeMarkdown(frontmatter, compiled_truth, timeline, {type, title, tags})`, and re-imports THAT, so re-chunking a DB-only page preserves everything while still bumping `chunker_version`. Pinned by `test/reindex-preserve-tags.test.ts`.
- `src/commands/reindex-code.ts` (v0.21.0 Cathedral II E2, extended v0.37.3.0) — `gbrain reindex --code [--source ID] [--dry-run] [--yes] [--json] [--force] [--no-embed]`. Walks `pages WHERE type = 'code'` in 100-row batches, replays through `importCodeFile` for chunk + embed + content_hash folding. Idempotent unless `--force` bypasses the content_hash early-return. **v0.37.3.0:** cost-preview model field now reads `getEmbeddingModelName()` from the gateway instead of the back-compat `EMBEDDING_MODEL` constant — preview reflects what the gateway will actually embed with. Same wave adds an informational stderr nudge inside `runReindexCode` (not the CLI wrapper, so dry-run + execute both surface it): when the configured embedding model isn't code-tuned (allowlist currently `{'voyage-code-3'}`, case-insensitive bare match against gateway-returned name), prints a 4-line recommendation to switch to `voyage:voyage-code-3`. Suppress with `GBRAIN_NO_CODE_MODEL_NUDGE=1`, `--no-embed`, or `--json`. Pure `shouldNudgeCodeModel(bareName)` helper returns a tagged `NudgeDecision` union; the helper takes the bare model name (matches gateway return shape) and emits qualified `voyage:voyage-code-3` for the paste-ready `gbrain config set` line. Pinned by `test/ai/voyage-code-3-recipe.test.ts`, `test/reindex-code-nudge.serial.test.ts`, and `test/reindex-code-model-source.serial.test.ts` (the latter is the IRON-RULE regression for the cost-preview fix).
- `src/commands/sync.ts:resolveSlugByPathOrSourcePath` (v0.32.7 CJK wave, codex post-merge F4) — Resolves a slug by `pages.source_path` first (returns the stored slug for frontmatter-fallback pages whose path doesn't derive a slug), then falls back to `resolveSlugForPath(path)`. Threaded into all 4 delete/rename call sites (`performSync`'s un-syncable cleanup at ~:531, deletes at ~:603, rename oldSlug at ~:622). Without this, emoji-only / Thai / Arabic filenames whose slug came from frontmatter would orphan on delete/rename (the delete path would compute the wrong path-derived slug). Best-effort query — pre-migration brains fall through to the legacy path.
- `src/core/utils.ts` — Shared SQL utilities extracted from postgres-engine.ts. Exports `parseEmbedding(value)` (throws on unknown input, used by migration + ingest paths where data integrity matters) and as of v0.12.3 `tryParseEmbedding(value)` (returns `null` + warns once per process, used by search/rescore paths where availability matters more than strictness). **v0.26.9 (D14):** adds `isUndefinedColumnError(err)` predicate — pattern-matches Postgres SQLSTATE 42703 / "column ... does not exist" with engine-driver shape variation tolerated. Replaces bare `catch {}` blocks in `oauth-provider.ts` so genuine errors (lock timeout, network blip, permission denied) propagate while column-missing falls through to the legacy fallback path. Reusable from any future code that needs the same column-existence probe semantics. **v0.32.8 (PR #860):** adds `validateSourceId(id)` that throws on anything outside `^[a-z0-9_-]+$`. Used by the per-source disk-layout fix in patterns.ts/synthesize.ts before any `join(brainDir, '.sources', source_id, slug+'.md')` call so source_id can't traverse out of brainDir. `rowToPage` updated to populate the now-required `Page.source_id` field from the SELECT projection (`scripts/check-source-id-projection.sh` enforces that every projection feeding `rowToPage` includes the column).
- `src/core/db.ts` — Connection management, schema initialization. v0.22.1 (#363, contributed by @orendi84): `resolveSessionTimeouts()` returns `statement_timeout` + `idle_in_transaction_session_timeout` (defaults: 5min each, env-overridable via `GBRAIN_STATEMENT_TIMEOUT` / `GBRAIN_IDLE_TX_TIMEOUT` / `GBRAIN_CLIENT_CHECK_INTERVAL`). Both `connect()` (module singleton) and `PostgresEngine.connect()` (worker pool) consume the result via postgres.js's `connection` option, sending GUCs as startup parameters that survive PgBouncer transaction mode (unlike the prior `setSessionDefaults` post-pool SET, kept as a back-compat no-op shim).
- `src/commands/migrate-engine.ts` — Bidirectional engine migration (`gbrain migrate --to supabase/pglite`)
- `src/core/import-file.ts` — importFromFile + importFromContent (chunk + embed + tags). **v0.41.31.0:** `importFromContent` and `importCodeFile` stamp `pages.embedding_signature` via `setPageEmbeddingSignature(slug, {sourceId, signature: currentEmbeddingSignature()})` when the import actually embedded (not `--no-embed`) — covers the inline import/sync path so a model/dims swap is detectable as stale. `importCodeFile` only stamps when every chunk was freshly embedded this call (`needsEmbedIndexes.length === chunks.length`); mixed reuse-by-hash pages stay unstamped (`reindex --code --force` / `embed --stale` handle the swap for those). **v0.41.37.0 (#1621):** `importFromContent`'s tag reconciliation is now ADD-ONLY. The pre-fix "remove every existing tag not in current frontmatter, then add current" logic wiped ALL DB-side enrichment tags (auto-tag / dream synthesize / signal-detector) on every re-import — most visibly under `gbrain reindex --markdown`, which re-imports every page with `forceRechunk`. The `tags` table has no provenance column and frontmatter tags are stripped from stored `pages.frontmatter` (markdown.ts:118), so at re-import time a frontmatter-origin tag can't be distinguished from a DB-enrichment tag — deletion is unsafe. Now it only `addTag` (idempotent, ON CONFLICT DO NOTHING). Accepted trade-off: removing a tag from frontmatter no longer removes it from the DB on next sync (needs a `tag_source` provenance column, deferred — TODOS.md #1621-followup). Pinned by `test/reindex-preserve-tags.test.ts` + `test/import-file.test.ts`.
- `src/core/sync.ts` — Pure sync functions (manifest parsing, filtering, slug conversion). **v0.35.5.0:** new exported `pruneDir(name: string): boolean` helper is the single source of truth for descent-time directory exclusion across walkers. Blocks `node_modules` (no leading dot, so pre-v0.35.5 walkers slipped through and inflated MISSING_OPEN counts via vendor packages), dot-prefix dirs, `ops/`, and `*.raw` sidecars. `isSyncable` now applies it per path segment; `walkMarkdownFiles` in `src/commands/extract.ts` and `listTextFiles` in `src/core/cycle/transcript-discovery.ts` consult it BEFORE recursing so the IO cost of walking thousands of vendor files is saved. Closes #923 + #202. `manageGitignore` worktree fix in same wave: discriminator now matches the gitdir path segment (`/modules/<name>` = submodule, `/worktrees/<name>` = worktree, per Git's documented layout) instead of the legacy absolute-vs-relative check that misclassified absorbed submodules and worktrees both. Conductor worktrees are first-class repos and now get `.gitignore` management for storage-tiering. Closes #889. v0.22.12 (#500, foundation by @wintermute via #501): `classifyErrorCode(errorMsg)` regex-based classifier with 12 codes (`SLUG_MISMATCH`, `YAML_PARSE`, `YAML_DUPLICATE_KEY`, `MISSING_OPEN`, `MISSING_CLOSE`, `NESTED_QUOTES`, `EMPTY_FRONTMATTER`, `NULL_BYTES`, `INVALID_UTF8`, `STATEMENT_TIMEOUT`, `FILE_TOO_LARGE`, `SYMLINK_NOT_ALLOWED`) plus `UNKNOWN` fallback. `summarizeFailuresByCode(failures)` returns sorted `[{code, count}]`. `code?` optional field on `SyncFailure`; backfilled at ack time on pre-v0.22.12 entries. `acknowledgeSyncFailures()` returns `AcknowledgeResult { count, summary }`. Three regexes (`MISSING_OPEN`, `MISSING_CLOSE`, `EMPTY_FRONTMATTER`) broadened to match actual `markdown.ts:159-244` validator message strings, not just the literal code-name prefix. `FILE_TOO_LARGE` covers all three production size sites in `import-file.ts:199, 352, 401`; `SYMLINK_NOT_ALLOWED` covers the rejection at `:347`. Closes the silent-skip pattern that motivated #500.
- `src/core/storage.ts` — Pluggable storage interface (S3, Supabase Storage, local)
- `src/core/storage-config.ts` (v0.22.11) — Storage tiering: `loadStorageConfig` reads `gbrain.yml`, normalizes deprecated keys (`git_tracked` / `supabase_only`) to canonical (`db_tracked` / `db_only`) with once-per-process deprecation warning, and runs `normalizeAndValidateStorageConfig` (auto-fixes missing trailing `/`, throws `StorageConfigError` on tier overlap). Path-segment matcher: `media/x/` does NOT match `media/xerox/foo`. Replaces gray-matter (broken on delimiter-less YAML) with a dedicated parser for the `gbrain.yml` shape.
- `src/core/disk-walk.ts` (v0.22.11) — `walkBrainRepo(repoPath)` returns `Map<slug, {size, mtimeMs}>` from one recursive `readdirSync`. Skips dot-dirs, `node_modules`, non-`.md` files. Used by `gbrain storage status` to replace per-page `existsSync + statSync` (~400K syscalls on 200K-page brains → tens).
- `src/core/git-head.ts` (v0.41.27.0) — local git HEAD freshness probe for `gbrain doctor`. `isSourceUnchangedSinceSync(localPath, lastCommit, opts?)` returns true iff `localPath` is a git repo whose current HEAD matches `lastCommit`; when `opts.requireCleanWorkingTree` is true, also requires the working tree to have no uncommitted changes (mirrors `gbrain sync`'s force-walk gate at `sync.ts:1075` so doctor and sync agree on "is there work to do?"). Two probe seams (`_setGitHeadProbeForTests`, `_setGitCleanProbeForTests`) match the `last-retrieved.ts` precedent so unit tests stay R2-compliant (no `mock.module`). Uses `execFileSync` with array args — shell metachars in `local_path` cannot escape to a shell (the v0.41.27.0 superseded PR #1564 used `execSync` through `/bin/sh -c` with `JSON.stringify` for shell-escape, which is unsafe; the rebuild's regression test runs real `execFileSync` against `'/nonexistent/$(touch <sentinel>)/repo'` and asserts the sentinel file is never created). Fail-open on every error: missing path, not a git repo, git not installed, timeout, NULL inputs, dirty-probe errored → returns false, preserving the caller's prior time-based behavior. Chunker-version-match check lives in the caller (doctor.ts) because it depends on engine state (`sources.chunker_version` vs `CHUNKER_VERSION` from `src/core/chunkers/code.ts`). Designed for reuse: autopilot's per-source dispatch will want the same gate (filed as v0.41.27.1+ TODO in the plan). Pinned by `test/core/git-head.test.ts` (14 cases incl. the shell-injection regression guard). **v0.41.32.0 (supersedes #1623):** `GitFreshnessOpts.requireCleanWorkingTree` widened `boolean → boolean | 'ignore-untracked'`. In `'ignore-untracked'` mode the clean probe runs `git status --porcelain --untracked-files=no`, so a quiet repo with stray untracked dirs (`?? companies/`, `?? media/`) is still "unchanged" — sync's incremental path keys off the commit diff and never imports untracked files, so doctor agrees with sync. `GitCleanProbe` gains an `ignoreUntracked?` second arg. One-line headline fix for the false-SEVERE staleness bug.
- `src/core/source-health.ts` (v0.40, extended v0.41.32.0) — per-source health metrics for `gbrain sources status` + doctor's `federation_health`. **v0.41.32.0 (supersedes #1623):** commit-relative staleness. New `newestCommitMs(localPath)` = HEAD committer time via `git log -1 --format=%ct` (fail-open null; NO working-tree mtime parsing — committed content only, robust against the porcelain-mtime bug farm). New pure `lagFromContentMs(contentMs|null, lastSyncMs|null, nowMs)` = remote/column comparator (null lastSync → null; negative wall-clock → skew passthrough; `contentMs <= lastSync` → 0; else/null-content → wall-clock). `computeAllSourceMetrics(engine, sources, {probeContent?})`: LOCAL (`probeContent:true`, `gbrain sources status`) → `isSourceUnchangedSinceSync(..., {requireCleanWorkingTree:'ignore-untracked'}) ? 0 : wall-clock` (live commit-hash, catches HEAD moving to an old-dated commit which a timestamp compare would miss); REMOTE (default, `federation_health` on the HTTP MCP path) → `lagFromContentMs(row.newest_content_at, ...)`, NO git subprocess (v0.41.27.0 trust boundary). Dead `isSourceStale(src, intervalMs)` removed (only `autopilot-fanout.ts`'s own variant is live). Pinned by `test/source-health.test.ts`.
- `src/core/git-remote.ts` (v0.35.3.0) — SSRF-hardened git invocations for remote-source `cloneRepo` and `pullRepo`. Exports two distinct flag constants because `git`'s argv grammar treats them differently: `GIT_SSRF_FLAGS` (3 `-c` config flags — `protocol.allow=user`, `protocol.file.allow=never`, `http.allowRedirects=false`) is **global config**, spread BEFORE the subcommand verb. New `GIT_SSRF_SUBCOMMAND_FLAGS = ['--no-recurse-submodules']` is **subcommand-scoped**, spread AFTER the verb. Pre-v0.35.3 a single combined `GIT_SSRF_FLAGS` array spread `--no-recurse-submodules` before the verb where real git rejects it with exit 129 ("unknown option"); the fake-git test harness exited 0 regardless of argv shape, so CI missed it for ~7 months and every remote-source clone/pull was silently broken. `cloneRepo` argv: `git <GIT_SSRF_FLAGS> clone <GIT_SSRF_SUBCOMMAND_FLAGS> --depth=1 [--branch X] -- <url> <dir>`. `pullRepo` argv: `git <GIT_SSRF_FLAGS> -C <dir> pull <GIT_SSRF_SUBCOMMAND_FLAGS> --ff-only`. Pinned by `test/git-remote.test.ts` position-anchored regression guard (`argv.indexOf('--no-recurse-submodules') > argv.indexOf(verb)`).
- `src/commands/storage.ts` (v0.22.11) — `gbrain storage status [--repo P] [--json]`. Split into pure data (`getStorageStatus`) + JSON formatter + human formatter (ASCII-only per D10) matching the `orphans.ts` pattern. `PageCountsByTier` and `DiskUsageByTier` are distinct nominal types so swaps fail at compile time.
- `gbrain.yml` (brain repo root, v0.22.11) — Optional storage tiering config. Top-level `storage:` section with `db_tracked:` and `db_only:` array-valued keys. `gbrain sync` auto-manages `.gitignore` for `db_only` paths on successful sync (skips on dry-run, blocked-by-failures, submodule context, or `GBRAIN_NO_GITIGNORE=1`). `gbrain export --restore-only [--repo P] [--type T] [--slug-prefix S]` repopulates missing `db_only` files from the database.
- `src/core/supabase-admin.ts` — Supabase admin API (project discovery, pgvector check)
- `src/core/file-resolver.ts` — File resolution with fallback chain (local -> .redirect.yaml -> .redirect -> .supabase)
- `src/core/chunkers/` — 3-tier chunking (recursive, semantic, LLM-guided). v0.19.0 adds `code.ts` — tree-sitter-based semantic chunker for 30 languages (v0.41 added SQL via DerekStride/tree-sitter-sql) with embedded-asset WASMs (`src/assets/wasm/`), `@dqbd/tiktoken` cl100k_base tokenizer, small-sibling merging. `CHUNKER_VERSION` constant folded into `importCodeFile`'s `content_hash` so chunker shape changes force clean re-chunks across releases. **v0.41 D2 SQL wave (#1173):** `extractSymbolName` gains an inline SQL branch (`extractSqlSymbolName`) that dives through DerekStride's `statement` wrapper into the inner DDL child (`create_table`/`create_function`/`create_view`/`create_index`/`create_procedure`/`create_type`/`create_schema`/`create_database`/`create_trigger`/`alter_table`/`alter_view`) and extracts the target identifier via the `name` field with identifier-shaped fallback. DML kinds (`select`/`insert`/`update`/`delete`/`merge`/`with`) deliberately return null so chunks emit unnamed — code-def is a DDL signal. `normalizeSymbolType` gains parallel SQL branches mapping `create_table → 'table'`, `create_view → 'view'`, etc. `src/commands/code-def.ts:DEF_TYPES` was extended in the same wave with `'table' | 'view' | 'index' | 'procedure' | 'schema' | 'database' | 'trigger'` so the new chunks surface in `gbrain code-def <name>` queries.
- `src/core/errors.ts` (v0.19.0) — `StructuredAgentError` + `buildError` + `serializeError`. Every new v0.19.0 agent-facing surface (code-def, code-refs, usage errors) uses this envelope; matches v0.17.0 `CycleReport.PhaseResult.error` shape.
- `src/assets/wasm/` (v0.19.0, extended v0.41) — 37 tree-sitter grammar WASMs + tree-sitter runtime. Committed to the repo so `bun --compile` embeds them deterministically via `import path from ... with { type: 'file' }`. The CI guard `scripts/check-wasm-embedded.sh` fails the build if the compiled binary ever silently falls through to recursive chunks. **v0.41 D2 wave (#1173):** `tree-sitter-sql.wasm` (DerekStride/tree-sitter-sql @ c2e1e08db1ea20dc23bdb8d228a81a8756e9c450, built with tree-sitter-cli@v0.26.3 --abi 14) adds SQL coverage at 11 MB — substantially larger than peers because the grammar covers PostgreSQL + MySQL + SQLite + T-SQL basics (40 MB of generated parser.c). The compiled gbrain binary grows ~6% as a result; tracked as a follow-up TODO whether to switch to a smaller-coverage grammar.
- `src/commands/code-def.ts` + `src/commands/code-refs.ts` (v0.19.0) — symbol definition + references lookup. Query `content_chunks.symbol_name` or chunk_text ILIKE with `page_kind='code'` filter. Auto-JSON when stdout is not a TTY (gh-CLI convention). Bypass the standard `searchKeyword` `DISTINCT ON (slug)` collapse so multiple call-sites from the same file surface.
- `src/core/search/` — Hybrid search: vector + keyword + RRF + multi-query expansion + dedup. As of v0.22.0, `searchKeyword` / `searchKeywordChunks` / `searchVector` apply source-aware ranking at the SQL layer (curated content like `originals/`, `concepts/`, `writing/` outranks bulk content like `wintermute/chat/`, `daily/`, `media/x/`). `searchVector` uses a two-stage CTE so source-boost re-ranking doesn't kill the HNSW index. Hard-exclude prefixes (`test/`, `archive/`, `attachments/`, `.raw/` by default) filter at retrieval, not post-rank. Both gates honor `detail !== 'high'` so temporal queries surface chat pages normally.
- `src/core/search/intent.ts` — Query intent classifier (entity/temporal/event/general → auto-selects detail level)
- `src/core/search/eval.ts` — Retrieval eval harness: P@k, R@k, MRR, nDCG@k metrics + runEval() orchestrator
- `src/core/search/source-boost.ts` (v0.22.0) — Source-type boost map keyed by slug prefix. `DEFAULT_SOURCE_BOOSTS` (originals/ 1.5, concepts/ 1.3, writing/ 1.4, people/companies/deals/ 1.2, daily/ 0.8, media/x/ 0.7, wintermute/chat/ 0.5) and `DEFAULT_HARD_EXCLUDES` (test/, archive/, attachments/, .raw/). `parseSourceBoostEnv` / `parseHardExcludesEnv` parse comma-separated `prefix:factor` pairs from `GBRAIN_SOURCE_BOOST` / `GBRAIN_SEARCH_EXCLUDE` env vars. `resolveBoostMap` and `resolveHardExcludes` merge defaults + env + caller `SearchOpts.exclude_slug_prefixes`/`include_slug_prefixes`.
- `src/core/search/sql-ranking.ts` (v0.22.0, extended v0.41.34.0) — Pure SQL string builders. `buildSourceFactorCase(slugColumn, boostMap, detail)` emits a CASE expression with longest-prefix-match wins (returns literal `'1.0'` when `detail === 'high'` for temporal-bypass parity with COMPILED_TRUTH_BOOST). `buildHardExcludeClause(slugColumn, prefixes)` emits `NOT (col LIKE 'p1%' OR col LIKE 'p2%')` — OR-chain wrapped in NOT, NOT `NOT LIKE ALL/ANY` (those quantifiers don't express set-exclusion). LIKE meta-character escape covers all three of `%`, `_`, AND `\` (backslash matters because it's Postgres LIKE's default escape char). Single-quote doubling on SQL string literals so injection-style inputs are inert text. **v0.41.34.0 (retrieval-maxpool incident, T1):** new `buildBestPerPagePoolCte(...)` is the shared per-page max-pool CTE both engines' `searchVector` inject — instead of returning the single best chunk per page from an inner `ORDER BY embedding <=> vec LIMIT N` (which let a page lose to a neighbor on ONE weak chunk while its strong chunk sat just below the inner cut), the CTE pools the BEST chunk score per `(source_id, slug)` composite key, so a page surfaces on its strongest evidence. Composite key (not bare slug) keeps multi-source brains correct. Single source of truth so the two engines can't drift on the pooling SQL.
- `src/core/search/title-match.ts` (v0.41.34.0, retrieval-maxpool incident, T2) — pure, zero-I/O title-phrase matcher shared by the production title boost AND NamedThingBench (no drift). `isTitlePhraseMatch(query, title)` returns true when the normalized query is a contiguous token run inside the title with `>= MIN_CONTENT_TOKENS=2` non-stopword tokens, OR an exact full-title match (covers deliberate 1-word chosen names like "Mingtang"). Token-boundary matching (never raw substring, so "art" doesn't match "Bartholomew"); small conservative English stopword set excluded from the content-token floor (Codex#10 guard against promoting generic pages on stopword-y queries); NFKC normalize so CJK / width variants converge. Exports `tokenizeTitle` + `__test__` internals. Closes the direct regression: "Greek amphitheater" matched a weak body chunk instead of the page whose title contained the phrase.
- `src/core/search/alias-normalize.ts` (v0.41.34.0, retrieval-maxpool incident, T3) — ONE normalizer shared by the WRITE path (ingest projects frontmatter `aliases:` into `page_aliases`) and the READ path (search matches query against `page_aliases`), so stored aliases can't silently fail to match queries via divergent normalization (same single-source posture as `cjk.ts`). `normalizeAlias(raw)` does NFKC + lowercase + whitespace-collapse + trim + strip one layer of wrapping quotes/brackets; returns `''` for empty (callers MUST skip empty aliases). `normalizeAliasList(value)` coerces a frontmatter scalar / array / comma-list / garbage into a deduped list of normalized non-empty aliases — used by both the ingest projection and the `reindex --aliases` backfill.
- `src/core/search/evidence.ts` (v0.41.34.0, retrieval-maxpool incident, T4) — the agent-facing why-it-matched contract that closes the incident's root behavior (agent read one blended score 0.64, decided "no strong match, safe to create", wrote a duplicate over a fully-developed page). `classifyEvidence(r)` names the strongest signal (precedence: `alias_hit` > `exact_title_match` > `high_vector_match` (base ≥ `HIGH_MATCH_FLOOR=0.85`) > `keyword_exact` (base ≥ `SOLID_MATCH_FLOOR=0.6`) > `weak_semantic`). `createSafetyFor(evidence)` derives the don't-duplicate hint (`exists` / `probable` / `unknown`) the agent keys off INSTEAD of a raw threshold (a blended RRF/cosine score is not a calibrated probability, Codex#5). `stampEvidence(results)` stamps `evidence` + `create_safety` in place once at pipeline end (after the alias hop, before slice); idempotent.
- `src/core/search/mode.ts` extension (v0.41.34.0, retrieval-maxpool incident, T2) — new `title_boost: number | undefined` knob in `ModeBundle` (default `1.25` for all three modes; multiplier for the post-fusion title-phrase boost). Override chain: per-call `SearchOpts` → `search.title_boost` config (clamped `[1.0, 5.0]`) → bundle. `KNOBS_HASH_VERSION` bumps 6→7 with a `tib=` parts entry so a title-boost-on cache write can't be served to a title-boost-off lookup. `SEARCH_MODE_CONFIG_KEYS` gains `search.title_boost`.
- `src/commands/search-diagnose.ts` (v0.41.34.0, retrieval-maxpool incident, T0) — `gbrain search diagnose "<query>" --target <slug> [--json] [--source <id>]`: Phase-0 retrieval diagnostic. Traces WHERE a target page surfaces (or fails to) across keyword / vector (per-page max-pool) / alias / hybrid layers and names the layer responsible for an incident, so an operator can pin whether the fix is max-pool/innerLimit (vector) vs title/alias. The verdict names the layer that DOES surface the target (or "none"). Pinned by `test/search/search-diagnose.test.ts`.
- `src/commands/reindex-aliases.ts` (v0.41.34.0, retrieval-maxpool incident, T8) — `gbrain reindex --aliases [--limit N] [--dry-run] [--json] [--source <id>]`: backfills the free-text alias layer for EXISTING pages whose frontmatter `aliases:` predate v110 (the import-time projection covers new + changed pages). Reads each page's frontmatter `aliases:`, writes via `engine.setPageAliases`. Idempotent + convergent (setPageAliases replaces a page's alias set) so no op-checkpoint needed; walks `listAllPageRefs` (cheap cross-source enumeration), `--source` narrows. Pinned by `test/search/reindex-aliases.test.ts`.
- `src/eval/retrieval-quality/harness.ts` + `src/commands/eval-retrieval-quality.ts` + `test/fixtures/retrieval-quality/namedthing.jsonl` (v0.41.34.0, retrieval-maxpool incident, T6) — NamedThingBench, the retrieval-quality eval that makes the incident impossible to reintroduce silently. Seven query families, each a distinct failure class: `title-substring` (the direct regression), `generic-to-named` (tourist label → named thing), `alias-synonym` (declared alias / romanization → canonical), `multi-chunk-dilution` (one strong chunk among many weak — stresses max-pool), `short-vs-rich`, `graph-relationship` (guardrail), `hard-negative` (precision guard, must NOT return a page). `gbrain eval retrieval-quality <fixture.jsonl>` runs it; hard gates (e.g. title-substring Hit@1 ≥ 0.95, alias Hit@1 ≥ 0.98, multi-chunk-dilution Hit@3 = 1.0). Pure: caller injects a `SearchFn` (CLI uses `hybridSearch`, tests stub) so it's engine-agnostic. Metric glossary entries (`hit@1` / `hit@3`) added to `src/core/eval/metric-glossary.ts`. Pinned by `test/eval-retrieval-quality.test.ts` + `test/retrieval-quality-harness.test.ts`.
- `docs/architecture/RETRIEVAL.md` + `docs/architecture/RETRIEVAL_MAXPOOL_INCIDENT.md` (v0.41.34.0) — retrieval-pipeline architecture reference + the named-thing-miss incident write-up (root cause, the five-layer fix, the eval that pins it).
- `src/core/types.ts` extension + `src/core/operations.ts:search` + `src/core/import-file.ts` + `src/cli.ts` + `src/core/search/telemetry.ts` (v0.41.34.0, retrieval-maxpool incident) — the wiring layer for the cathedral. `SearchResult` gains `evidence`, `create_safety`, `title_match_boost`, and `alias_hit` (all optional; evidence/create_safety reference the union types in `evidence.ts`). The `search` MCP op (T4/D4/D15) switches from keyword-only to a cheap-hybrid path by default and accepts a per-call `mode` (conservative|balanced|tokenmax) honored ONLY for trusted/local callers (`resolvePerCallMode(ctx, ...)` — remote callers use the configured mode so a remote provider can't force tokenmax spend); every search path stamps evidence fail-soft. `importFromContent` projects frontmatter `aliases:` into `page_aliases` via `normalizeAliasList` + `engine.setPageAliases` (T3 WRITE side) so new + changed pages register aliases at ingest. `src/cli.ts` adds the `gbrain search diagnose` dispatch (lazy import) and reconciles the `search` CLI path with the cheap-hybrid op. `src/core/search/telemetry.ts` extends the rollup with the T7 rank-1 base_score drift signal (sum/count + 3 coarse buckets, aggregate not per-query per D10) surfaced via `gbrain search stats`, backed by migration v111's `search_telemetry` columns. Tests: `test/cli-search-dispatch.test.ts`, `test/search/per-call-mode.test.ts`, `test/search/telemetry-rank1.test.ts`, `test/search/title-boost-stage.test.ts`, `test/search/alias-hop.test.ts`, `test/search/evidence.test.ts`, `test/search/searchvector-maxpool.test.ts`, `test/search/pre-migration-failopen.test.ts`.
- `src/commands/eval.ts` — `gbrain eval` command: single-run table + A/B config comparison. v0.25.0 adds sub-subcommand dispatch on `args[0]` so `gbrain eval export` + `gbrain eval prune` + `gbrain eval replay` route into session-capture handlers; bare `gbrain eval --qrels …` fall-through preserves the legacy IR-metrics flow. v0.27.x adds `gbrain eval cross-modal` to the dispatch (the user-facing path is the cli.ts no-DB branch — `src/commands/eval.ts:cross-modal` only fires when callers re-enter with an existing engine).
- `src/commands/eval-cross-modal.ts` (v0.27.x, extended v0.40.1.0 Track D) — multi-model quality gate. Three different-provider frontier models score the OUTPUT against the TASK on a 5-dim list. Verdict `pass` (exit 0) / `fail` (exit 1) / `inconclusive` (exit 2; <2/3 model successes per Q3=A in plans/radiant-napping-lerdorf.md). Reuses `src/core/ai/gateway.ts:chat()` so config/auth/aliasing comes from the gateway recipe registry — no parallel provider stack. Self-configures the gateway (`configureGateway(loadConfig() + process.env)`) since the cli.ts dispatch bypasses `connectEngine()`. Default cycles 3 in TTY, 1 in non-TTY (T11=B partial cost guardrail). Receipts land at `gbrainPath('eval-receipts')/<slug>-<sha8-of-output>.json`. The full `--budget-usd` cap is a v0.27.x follow-up TODO. **v0.40.1.0 Track D (T3+T4, per D1/D5/D6/D10):** new `--batch <jsonl> [--limit N] [--concurrent N] [--max-usd FLOAT] [--yes]` flags fan out cross-modal scoring across a LongMemEval-shape JSONL. Mutually exclusive with `--task` (fail-fast usage error if both set). Filters `kind: "by_type_summary"` rows from the input (Codex #6). Pre-flight cost estimate refuses if `> --max-usd` without `--yes`; default cap 5.00 USD. Semaphore-bounded fan-out via inline `runWithLimit<T>(items, limit, fn)` (~15 LOC, exported for unit tests): max N questions in-flight at once × 3 model slots = ceiling of 3N parallel API calls (default `--concurrent 3` → 9). Per-question receipts land in a per-batch tempdir and are deleted at end of run (per D10 — keeps `~/.gbrain/eval-receipts/` clean); the summary receipt inlines per-question verdicts as JSON, not file paths. Exit precedence (NEW batch-level policy, NOT inherited from aggregate.ts): ERROR > FAIL > INCONCLUSIVE > PASS. DI seam: `runEvalCrossModal(args, opts?: {runEval?: typeof runEval})` mirrors `runEvalLongMemEval(args, {client?})` at eval-longmemeval.ts:299; tests pass `opts.runEval` to bypass real LLM calls AND the gateway availability check. Pinned by 15 cases in `test/eval-cross-modal-batch.test.ts`.
- `src/core/cross-modal-eval/json-repair.ts` (v0.27.x) — `parseModelJSON(raw)` named export with a 4-strategy fallback chain (direct parse → fence-strip → trailing-comma + single-quote + embedded-newline repair → regex nuclear option). Adversarial input throws rather than fabricating scores — the aggregator treats a throw as "this model contributed nothing this cycle" so the gate stays correct at >=2/3 successes.
- `src/core/cross-modal-eval/aggregate.ts` (v0.27.x) — pure verdict logic. Pass criterion: `(successes >= 2) AND (every dim mean >= 7) AND (every dim min across models >= 5)` (Q2=A floor). Inconclusive when <2/3 models returned parseable scores (Q3=A regression guard for the v1 .mjs `Object.values({}).every(...) === true` empty-array PASS bug).
- `src/core/cross-modal-eval/runner.ts` (v0.27.x) — orchestrator. Each cycle runs `Promise.allSettled([gwChat(slotA), gwChat(slotB), gwChat(slotC)])` (T4=A — bare allSettled, no rate-leases for the CLI path; minion-integration TODO recovers cross-process concurrency). Stops early on PASS or INCONCLUSIVE; runs up to 3 cycles. Default slots: `openai:gpt-4o` / `anthropic:claude-opus-4-7` / `google:gemini-1.5-pro`. `estimateCost()` exports a small per-model pricing table (drifts; refresh alongside model-family bumps).
- `src/core/cross-modal-eval/receipt-name.ts` (v0.27.x) — receipt filename binds (slug, SKILL.md sha-8). `findReceiptForSkill(skillPath, receiptDir)` returns `'found' | 'stale' | 'missing'` (T10=A). Skillify-check item 11 surfaces the status as informational (T7=C); the audit does NOT fail on missing/stale receipts.
- `src/core/cross-modal-eval/receipt-write.ts` (v0.27.x) — wraps `fs.writeFileSync` with `mkdirSync({recursive:true})` ahead of every write (T5 correction; `gbrainPath()` does NOT auto-mkdir).
- `src/commands/eval-export.ts` (v0.25.0) — streams `eval_candidates` rows as NDJSON to stdout with `schema_version: 1` prefix on every line. EPIPE-safe, progress heartbeats on stderr, stable id-desc tiebreaker so `--since` windows never dupe/miss rows.
- `src/commands/eval-prune.ts` (v0.25.0) — explicit retention cleanup. Requires `--older-than DUR`. `--dry-run` reports would-delete count.
- `src/commands/eval-replay.ts` (v0.25.0, extended v0.41.0.0) — contributor-facing replay tool. Reads NDJSON from `gbrain eval export`, re-runs each captured `query` / `search` op against the current brain, computes set-Jaccard@k between captured + current `retrieved_slugs`, top-1 stability rate, and latency Δ. Stable JSON shape (`schema_version: 1`) for CI gating; human mode prints a regression table. Pure Bun, zero new deps. The dev-loop half of BrainBench-Real that closes the gap between "data captured" and "data used to gate a PR." See `docs/eval-bench.md` for the workflow. **v0.41.0.0 changes:** `parseNdjson` now skips lines where `_kind === 'baseline_metadata'` so `gbrain bench publish`-written baselines parse cleanly without the metadata header polluting row counts. New exported `replayCore(engine, opts): Promise<{summary, results}>` programmatic entrypoint + exported `ReplaySummary` type so `gbrain eval gate` can call replay in-process (NOT spawn subprocess — avoids gbrain-version-drift for source-tree CI runs). The existing CLI `runEvalReplay` now wraps `replayCore`.
- `src/core/bench/baseline-file.ts` + `src/core/bench/qrels-file.ts` + `src/core/bench/correctness-gate.ts` + `src/commands/bench-publish.ts` + `src/commands/eval-gate.ts` (v0.41.0.0) — the eval-loop wave. Two new CLI verbs: `gbrain bench publish --from <captured.ndjson> --to <X.baseline.ndjson>` writes a baseline file from `gbrain eval export` output (stamps stable `query_hash` on every row; metadata header carries `_kind: 'baseline_metadata'` + thresholds + `source_hash` + `baseline_mean_latency_ms`; deterministic sort by `(tool_name, query_hash)`; D4 strict posture — empty=fail, dupes=fail with paste-ready hint, `--to` exists=refuse without `--force`); `gbrain eval gate [--baseline X] [--qrels Y]` is the two-gate dispatcher (regression gate via in-process `replayCore`, correctness gate via bare `hybridSearch` for determinism per eng-D6, both must pass when both flags set, exit 0 PASS / 1 FAIL / 2 USAGE). Source-id-aware: `bench publish` dedup key is `(tool_name, source_ids, query_hash)`; qrels compare keys are `${source_id}::${slug}` everywhere; closes the multi-source-bug-class (canonical gbrain pitfall) at the file-shape layer. Latency math: `(baseline + delta) / baseline <= multiplier` (the original `delta / baseline` formula would have let 2.5x slowdowns pass at multiplier=2.0). D3 fail-closed: ANY in-process throw flips verdict to fail with named breach in `breaches[]` — never silently exit 0. `.qrels.json` shape preserves the existing 12-row `test/fixtures/eval-baselines/qrels-search.json` fixture (slug-only `relevant_slugs` + `first_relevant_slug` auto-promote to `source_id='default'`) AND supports the federated shape (explicit `relevant: [{source_id, slug}]` + `expected_top1`). `correctness-gate.ts` runs each qrels query via bare `hybridSearch`; per-query throw recorded as `errored: true` and flagged as gate failure (Finding 2D). Audit JSONL for bench-publish at `~/.gbrain/audit/bench-publish-YYYY-Www.jsonl`. Plan + 23 decisions + 2 codex outside-voice rounds at `~/.claude/plans/system-instruction-you-are-working-rustling-peacock.md`. Pinned by 65 cases across `test/bench/baseline-file.test.ts` (9) + `test/bench/qrels-file.test.ts` (19) + `test/bench/correctness-gate.test.ts` (6) + `test/bench-publish.test.ts` (10) + `test/eval-gate.test.ts` (10) + `test/eval-replay-metadata-skip.test.ts` (2) + `test/cycle/nightly-probe-adapters.test.ts` (6) + `test/autopilot-nightly-probe-wiring.test.ts` (8) + `test/e2e/eval-loop.test.ts` (4).
- `src/core/cycle/nightly-probe-adapters.ts` (v0.41.0.0) — bridges the autopilot's object-shape `NightlyProbeDeps` to the existing argv-shape `runEvalLongMemEval` + `runEvalCrossModal` CLI functions. Cross-modal adapter argv MUST include `--output summaryPath` (codex round-2 #1 — without it the summary lands at the default receipt path and the adapter would read nothing from `summaryPath`). In-process invocation (NOT subprocess) — avoids gbrain-version-drift class for source-tree CI runs. ~125 LOC. Pinned by `test/cycle/nightly-probe-adapters.test.ts` (6 cases including argv-shape regression for the `--output` fix).
- `src/commands/autopilot.ts` extension (v0.41.0.0) — tick body invokes `runNightlyQualityProbe` when `cfg.autopilot.nightly_quality_probe.enabled === true` (default OFF — opt-in to protect API spend on fresh installs). Per eng-D10 (codex round-1 #11): NO scheduler-side rate-limit check — `runNightlyQualityProbe`'s internal `shouldRunNightly` (reading the audit JSONL) is the single source of truth. Probe call wrapped in try/catch that logs via `logError` and DOES NOT bump `consecutiveErrors` (probe failure is informational, never crashes the loop). Default `max_usd` cap = 5. Source-shape pinned by `test/autopilot-nightly-probe-wiring.test.ts` (8 regression assertions).
- `test/eval-replay-gate.test.ts` + `test/fixtures/eval-baselines/qrels-search.json` (v0.40.1.0 Track D / T5, per D8 reshape) — hermetic retrieval qrels gate that runs in the standard PR unit-shard CI matrix (`.github/workflows/test.yml`, NOT the fixed-file E2E workflow). Structural replacement for the original "replay against captured `eval_candidates` baseline" design (deferred to `v0.41+: contributor-mode CI capture` in TODOS.md; Codex outside-voice caught three fatal flaws — select-e2e.ts is local-only, eval-export bypasses op-layer capture on PGLite-seed tests, replay re-embeds via gateway which needs an API key CI doesn't have). Uses the canonical PGLite block from CLAUDE.md test-isolation rules (R3+R4) and the basis-vector embedding pattern from `test/e2e/search-quality.test.ts:23-28` for fully hermetic retrieval. The qrels fixture (12 queries) is hand-curated with PLACEHOLDER names only (alice-example, widget-co-example, etc. — per Codex #9 + CLAUDE.md privacy rule) and embeds each query at a deterministic basis dimension so retrieval is reproducible. Each query lists `relevant_slugs[]` + `first_relevant_slug`; for each, the test computes `top1_match_rate` (top-1 == first_relevant) and `recall@10` (fraction of relevant_slugs in top-10), asserting both meet floors (defaults `>= 0.80` and `>= 0.85`). Env-overridable floors via `GBRAIN_REPLAY_GATE_TOP1_FLOOR` / `GBRAIN_REPLAY_GATE_RECALL_FLOOR` (with `withEnv()` per CLAUDE.md R1). Refresh discipline (per D4): when ranking changes intentionally move expected slugs, edit `qrels-search.json` directly and include a `Why:` line in the commit body so future maintainers can read the audit trail. Without `Why:`, the gate degrades to rubber-stamp within months. Pinned by 5 cases in `test/eval-replay-gate.test.ts` including a privacy-grep regression guard against real-name reintroduction.
- `src/core/cycle/nightly-quality-probe.ts` + `src/core/audit-quality-probe.ts` + `test/fixtures/longmemeval-nightly.jsonl` + `test/nightly-quality-probe.test.ts` (v0.40.1.0 Track D / T6+T7+T8, per D12) — opt-in nightly cross-modal quality probe. The phase runs `gbrain eval longmemeval --by-type` against the committed 10-question placeholder fixture, pipes the output through `gbrain eval cross-modal --batch --max-usd 5 --yes`, and writes one event per run to `~/.gbrain/audit/quality-probe-YYYY-Www.jsonl` (ISO-week-rotated, mirrors `audit-slug-fallback.ts`; honors `GBRAIN_AUDIT_DIR`). Default DISABLED — opt-in via `gbrain config set autopilot.nightly_quality_probe.enabled true` (prevents surprise API spend on `gbrain init`). 24h rate limit (the pure `shouldRunNightly(now, recentEvents, windowMs?)` function) skips with audit row `outcome: rate_limited` when a recent run exists. Embedding-key short-circuit: longmemeval needs `gateway.embedQuery()`, so the phase exits early with `outcome: no_embedding_key` + stderr warn when no provider is configured. Full DI surface via `NightlyProbeDeps` (`isEnabled`, `hasEmbeddingProvider`, `resolveMaxUsd`, `resolveRepoRoot`, `runLongMemEval`, `runCrossModalBatch`, `now`) so the unit test stubs every external effect — no PGLite, no real LLM calls, no env mutation outside `withEnv()`. Cost ceiling: $5/run × 30 nights ≈ $150/month worst-case; expected real cost ~$0.35/night × 30 ≈ $10.50/month. **Autopilot scheduler wiring deferred to v0.41+ follow-up (filed in TODOS.md)** — the phase is callable in isolation today; the cycle-loop dispatcher hasn't been wired to invoke it on the 24h cadence yet. New `nightly_quality_probe_health` doctor check (in `src/commands/doctor.ts` right after `slug_fallback_audit`) reads the last 7 days of audit events: SKIPPED when feature flag is off (with paste-ready enable command); OK when enabled + all PASS; WARN on any FAIL / ERROR / BUDGET_EXCEEDED in the window with per-outcome counts. Pinned by 14 cases in `test/nightly-quality-probe.test.ts` (rate-limit pure-function unit tests + DI-stubbed end-to-end phase tests across every outcome branch).
- `src/commands/eval-trajectory.ts` + `src/commands/founder-scorecard.ts` + `src/core/trajectory.ts` (v0.35.7) — temporal trajectory + founder scorecard. The wave that turns the v0.35.3.1 date-aware contradiction probe into a useful temporal substrate. `gbrain eval trajectory <entity>` shows the chronological typed-claim history (mrr/arr/team_size/etc) with regressions auto-flagged inline; `gbrain founder scorecard <entity>` rolls up claim_accuracy / consistency / growth_trajectory / red_flags into one JSON. Pure-function math lives in `trajectory.ts`: `detectRegressions(points, threshold)` walks consecutive metric-value pairs per metric (10% drop default, env override `GBRAIN_TRAJECTORY_REGRESSION_THRESHOLD`); `computeDriftScore(points)` returns `1 - mean(cosine(emb[i], emb[i-1]))` over existing embeddings (null when <3 embedded points). Backed by `BrainEngine.findTrajectory(opts)` — both Postgres and PGLite, single SQL query, deterministic `ORDER BY valid_from ASC, id ASC` (R3). Source-scoped via the v0.34.1.0 `sourceId` scalar / `sourceIds` array dual pattern (D-CDX-6); visibility-filtered for remote callers (D-CDX-1) — `recall`-equivalent posture. MCP op `find_trajectory` (read scope, NOT localOnly) registered after `find_experts`. Migration v67 adds four optional typed-claim columns (`claim_metric`, `claim_value`, `claim_unit`, `claim_period`) + a partial index on `(entity_slug, claim_metric, valid_from) WHERE claim_metric IS NOT NULL`. Fence widens from 10 to 14 cells when any row has typed data; renderer stays at 10 cells when none do (no churn diff on existing fences). Metric labels normalize to lowercase snake_case via `normalizeMetricLabel` (15-entry seed map for common founder metrics). The `consolidate` cycle phase gains semantic upsert keyed on `(page_id, claim, since_date)` — fixes the pre-existing F4 duplicate-takes bug where re-running the full cycle after `extract_facts` cleared `consolidated_at` would silently append duplicate takes via `MAX(row_num)+1`. Also writes chronological `valid_until` on each cluster's older facts. The `extract_facts` cycle phase batch-embeds via `gateway.embed()` before insert AND threads `pages.effective_date` as the `pageEffectiveDate` fallback for `valid_from` (precedence chain: fence-row > pageEffectiveDate > now()). The contradiction probe MUST NOT write `valid_until` — R1+R8 grep guard at `test/eval-contradictions/no-valid-until-write.test.ts` pins this. Codex outside-voice round caught F1 (v66 collision → v67), F2 (Haiku lives in `facts/extract.ts` not `extract-facts.ts` cycle phase), F3 (cycle didn't embed before insert), F4 (idempotency bug), F5+F6 (missed `fence-write.ts` caller + no Page object there → pageEffectiveDate is OPTIONAL), F7 (privacy regression — visibility filter added), F8 (ParsedFact needed typed-field extension for markdown system-of-record), F9 (dual scalar+federated sourceId). Plan: `~/.claude/plans/system-instruction-you-are-working-curious-jellyfish.md`. Tests: 258 across 12 files. **v0.40.2.0 (migration v89 `facts_event_type_column`):** `facts` table gains a nullable `event_type TEXT` column so the typed-claim substrate can carry event-shaped rows (`event_type='meeting'`, `'job_change'`, `'location_change'`) alongside metric-shaped rows. `TrajectoryPoint.event_type: string | null` projected by both PGLite and Postgres `findTrajectory` paths. `TrajectoryOpts.kind?: 'metric' | 'event' | 'all'` filter added (default `'all'`). Existing callers (`founder-scorecard`, `eval-trajectory`) pass `kind: 'metric'` explicitly for call-site clarity — no behavior change since both already defensively skipped NULL-metric rows in their per-metric math. Back-compat pinned by `test/regressions/v0_40_2_0-trajectory-backcompat.test.ts` (4 cases: byte-identical `computeFounderScorecard` + `computeTrajectoryStats` output with and without event rows). Engine parity in `test/engine-parity-event-type.test.ts` (6 cases). Plan: `~/.claude/plans/system-instruction-you-are-working-crystalline-owl.md`.
- `src/core/trajectory-format.ts` (v0.40.2.0) — shared `formatTrajectoryBlock(points, entitySlug, opts)` consumed by both `gbrain think` (production) and the LongMemEval harness (benchmark). Groups by `(metric ?? event_type)`, per-metric cap 20, total cap 100, knowledge_update intent annotates value-change rows with `(superseded prior)`. Emits a `<trajectory entity="...">` XML envelope — `INJECTION_PATTERNS` in `src/core/think/sanitize.ts` extended to escape `</trajectory>`, `<trajectory ...>` open tags, and attribute injection so adversarial fact text can't break out. Pinned by `test/trajectory-format.test.ts` (17 cases: grouping, caps, sanitization, supersession annotation, determinism, provenance, text-cap, adversarial `</trajectory>` escape).
- `src/core/think/intent.ts` + `src/core/think/entity-extract.ts` (v0.40.2.0) — pure `classifyIntent(question)` returns `'temporal' | 'knowledge_update' | 'other'` (regex-first, no LLM call, `'other'` fast path short-circuits with zero SQL). `extractCandidateEntities(question, retrievedSlugs)` pulls high-precision candidates from retrieved entity-prefix slugs (`people/`, `companies/`, `organizations/`) and medium-precision noun phrases from the question. Stop-word boundaries + leading-verb stripper handle "When did I last meet Marco" → `marco` cleanly. Both consumed by `runThink` and by the LongMemEval harness so the two paths cannot drift. Pinned by `test/think-intent.test.ts` (14) and `test/think-entity-extract.test.ts` (10).
- `src/commands/eval-suspected-contradictions.ts` + `src/core/eval-contradictions/{judge,runner,types,date-filter,cost-tracker,cache,severity-classify,cross-source,trends,calibration,judge-errors,auto-supersession,fixture-redact}.ts` (v0.32.6) — `gbrain eval suspected-contradictions [run|trend|review]`. Probe samples top-K retrieval pairs per query (cross-slug + intra-page chunk-vs-take), date pre-filters (3-rule layered — same-paragraph-dual-date overrides separation rule), LLM judge (query-conditioned per Codex; UTF-8-safe truncation; C1 confidence-floor double-enforcement; resolution_kind output drives M7 paste-ready commands), persistent cache keyed on `(chunk_a_hash, chunk_b_hash, model_id, prompt_version, truncation_policy)` (Codex outside-voice fix — prompt edits cleanly invalidate prior verdicts), Wilson 95% CI calibration on the headline percentage with `small_sample_note` when n<30, judge_errors as first-class typed counters (parse_fail/refusal/timeout/http_5xx/unknown — Codex fix to bias from silent skip), M5 trend writes to `eval_contradictions_runs`, M6 source-tier breakdown reuses `DEFAULT_SOURCE_BOOSTS` prefix logic, deterministic sampling (combined_score DESC + lex tiebreaker — stable cache hit-rate across re-runs). Hermetic via `judgeFn` + `searchFn` DI in the runner; never touches the real gateway in tests. Engine surface: `BrainEngine.listActiveTakesForPages` (P1 batched), `writeContradictionsRun` + `loadContradictionsTrend` (M5), `getContradictionCacheEntry` + `putContradictionCacheEntry` + `sweepContradictionCache` (P2). Schema migrations v51 + v52. MCP op `find_contradictions` (read scope, NOT localOnly, NOT in subagent allowlist — user-initiated only). M1 doctor check surfaces high-severity findings with paste-ready resolution commands. M2 synthesize phase pre-fetches latest probe's top-5-by-severity findings and threads them into `buildSynthesisPrompt` as an informational block. 226 hermetic unit tests + 12 real-Postgres E2E. Plan: `~/.claude/plans/system-instruction-you-are-working-hashed-dewdrop.md`. Architecture doc: `docs/contradictions.md`.
- `src/core/think/index.ts` (v0.35.5.0 — gateway adapter, extended v0.40.2.0) — `runThink` no longer instantiates `new Anthropic()` directly. The internal `LLMClient` instance is now built by a small adapter that wraps `gateway.chat()` from `src/core/ai/gateway.ts`, the canonical AI seam v0.31.12 established for chat/embed/expansion. Closes #952: stdio MCP launches (Claude Desktop, Cursor) don't inherit shell env, so the Anthropic SDK's env-only key resolution lost the key any user had set via `gbrain config set anthropic_api_key`. The gateway reads from `~/.gbrain/config.json` AND from env, so both paths work. Test seam preserved: `opts.client?: ThinkLLMClient` injection still works for the 12+ existing tests (`test/think-pipeline.serial.test.ts`, `test/think-gateway-adapter.test.ts`, etc.); `opts.stubResponse` continues to short-circuit before any LLM call. When neither key nor client is available, the graceful "no LLM available" stub still fires with the same `NO_ANTHROPIC_API_KEY` warning. v0.36.x TODO: drop `ThinkLLMClient` indirection entirely, migrate tests to `__setChatTransportForTests` seam from `src/core/ai/gateway.ts`. **v0.40.2.0 trajectory injection (default ON):** `runThink` orchestrates `classifyIntent(question)` → `extractCandidateEntities(question, retrievedSlugs)` → `findTrajectory` (5s `Promise.race` timeout per candidate, concurrency cap 3) → `formatTrajectoryBlock` from `src/core/trajectory-format.ts`. `buildThinkUserMessage` (in `src/core/think/prompt.ts`) extended with a `trajectory?: ThinkTrajectoryBlockOpts` slot that honors BOTH existing prompt orderings (calibration mode: retrieval → calibration → trajectory → question; default mode: question → retrieval → trajectory → instruction). No third ordering invented. The MCP `think` op handler extracts `sourceScopeOpts(ctx)` to scalar `sourceId` / `allowedSources` / `remote` fields on `RunThinkOpts` so federated-read OAuth clients can't see trajectory rows outside their source scope. New config key `think.trajectory_enabled` (default `true`) flips the entire path off. Any error in the trajectory path degrades to "no block injected" + `TRAJECTORY_INJECTION_FAILED` warning — the think call itself never crashes from trajectory. Production path skips `fallback_slugify` resolutions deliberately (avoid querying invented slugs); the LongMemEval harness accepts them because the extractor and lookup go through the same slugify path. Pinned by `test/think-trajectory-injection.test.ts` (7 cases: temporal injection with superseded-prior annotation, `'other'` short-circuit, `withTrajectory: false` bypass, `think.trajectory_enabled=false` bypass, empty-trajectory skip, `findTrajectory` throw caught by `Promise.allSettled`, TRAJECTORY_INJECTED warning count). Debug: `GBRAIN_THINK_DEBUG=1 gbrain think "..."` prints the spliced prompt to stderr.
- `src/core/operations.ts` extension (v0.35.5.0 orphans fix) — `findOrphanPages` (both engines) now filters `p.deleted_at IS NULL` on the candidate side AND adds `JOIN pages src ON src.id = l.from_page_id WHERE src.deleted_at IS NULL` to the EXISTS subquery on the link-source side. Pre-v0.35.5 the query filtered nothing on `deleted_at`, so soft-deleted pages (v0.26.5 soft-delete shipped without updating this query) appeared as orphans AND links from soft-deleted source pages still suppressed live pages from orphan results. Closes #1021. Pinned by `test/orphans.test.ts`'s soft-delete cases.
- `src/commands/eval-longmemeval.ts` + `src/eval/longmemeval/{harness,adapter,sanitize}.ts` (v0.28.1, extended v0.40.1.0 Track D and v0.40.2.0) — `gbrain eval longmemeval <dataset.jsonl>` runs the public [LongMemEval](https://huggingface.co/datasets/xiaowu0162/longmemeval) benchmark against gbrain's hybrid retrieval. Architecture: one in-memory PGLite per benchmark run created via `createBenchmarkBrain` + `withBenchmarkBrain` (NO `EphemeralBrain` class). Between questions, `TRUNCATE` over runtime-enumerated `pg_tables` so future schema migrations don't silently leak data across questions; infrastructure tables (`sources`, `config`, `gbrain_cycle_locks`, `subagent_rate_leases`) are preserved. `cli.ts` has a pre-dispatch bypass so `eval longmemeval` skips `connectEngine()` — the user's `~/.gbrain` brain is never opened. `--expansion` defaults to OFF (deterministic, no per-query Haiku call); pass `--expansion` to opt in. Default model resolves through `resolveModel()` 6-tier chain with `models.eval.longmemeval` as the new config key. Sanitization parity: `harness.ts` re-uses `INJECTION_PATTERNS` from `src/core/think/sanitize.ts` (now exported, line 22) so adding a pattern automatically covers takes AND benchmarks. Retrieved chat content is wrapped in `<chat_session id="..." date="...">` framing; the answer-gen system prompt declares the content UNTRUSTED. LLM injection seam: `runEvalLongMemEval(args, {client?: ThinkLLMClient})` lets tests stub the client so the full pipeline runs without an Anthropic API key. p50 25.9ms / p99 30.3ms warm reset+import+search on Apple Silicon (per `test/eval-longmemeval.test.ts` perf gate). Hand the JSONL output to LongMemEval's `evaluate_qa.py` to score (their published evaluator, not bundled — needs OpenAI gpt-4o per their spec). **v0.40.1.0 Track D (T1+T2, per D9):** per-question JSONL row gains `question: string` (additive — `evaluate_qa.py` ignores unknown fields) so the `gbrain eval cross-modal --batch` consumer has the `task` text without joining back against the source dataset. Each row also carries `question_type: string` and `recall_hit?: boolean` so a `--resume-from` run can rebuild the cumulative `recallByType` from the file alone. New `--by-type` flag emits a `{schema_version:1, kind:"by_type_summary", recall_by_type:{...}, aggregate:{...}}` line as the FINAL line of the output; resume-replace strips any prior summary at the tail so 5 resumed runs produce 1 summary, not 5 (Codex #7). Empty-bucket guard: `aggregate.rate` is `null` (not NaN) when no questions had ground truth. Optional `--by-type-floor F` (0..1) exits non-zero with a stderr line per breached `question_type`; default informational only. Pure `buildByTypeSummary(buckets)` + `emitByTypeSummary(path, summary)` + `seedRecallByTypeFromFile(path, bucket)` helpers exported for unit tests. Pinned by 5 new cases in `test/eval-longmemeval.test.ts`. **v0.40.2.0 inline Haiku extractor + trajectory routing (methodology change — read carefully):** new `src/eval/longmemeval/extract.ts` runs `extractAndInsertClaims()` over each haystack session before retrieval, populating the benchmark brain's `facts` table inline at import time. Single Haiku call per session with content-hash cache (cuts a 3-iteration benchmark run from $1.50 to $0.50 when sessions repeat across questions). Per-question alias map (fresh per question, never leaks across) — `"Marco"` + `"Marco Smith"` + `"marco"` collapse to one canonical slug via first-mention-wins. Fail-open on every error path (malformed JSON, Haiku throw, insert collision, empty array → `inserted: 0` without throwing). `getCacheStats()` writes empirical hit rate to stderr per run. New `src/eval/longmemeval/intent.ts` prefers the dataset's `question_type` label (`temporal-reasoning`, `knowledge-update`, etc.) before falling back to the SHARED regex set imported from `src/core/think/intent.ts` — single source of truth means think and longmemeval cannot drift. `runOneQuestion` routes temporal/knowledge_update intents through the shared `extractCandidateEntities` → `findTrajectory` → splice into the answer-gen prompt before the retrieved-sessions block. New CLI flag `--no-trajectory` bypasses BOTH the extractor and the intent routing (used by the measurement protocol to baseline default-on vs no-trajectory across 3 seeds per condition with paired-bootstrap CI). JSON envelope adds 5 per-question fields when trajectory routing is on: `intent`, `trajectory_points`, `entity_resolved`, `resolution_source`, `methodology_note`. The methodology_note also writes to stderr at run completion (`extractor=haiku-preprocess-full-haystack-v1`) — honest disclosure that the published gbrain LongMemEval number is "gbrain + Haiku-preprocess pipeline" vs "gbrain alone" so it's NOT directly comparable to baseline LongMemEval scores without that note. Pinned by `test/longmemeval-extract.test.ts` (13), `test/longmemeval-intent.test.ts` (9), `test/longmemeval-trajectory-routing.test.ts` (4 end-to-end through `runEvalLongMemEval` with both clients stubbed).
- `docs/eval-bench.md` (v0.25.0) — contributor guide for using captured data to benchmark retrieval changes before merging. Linked from CONTRIBUTING.md under "Running real-world eval benchmarks (touching retrieval code)".
- `src/core/eval-capture.ts` (v0.25.0) — op-layer capture wrapper called from `src/core/operations.ts` `query` + `search` handlers. Catches MCP + CLI + subagent tool-bridge from one site. Fire-and-forget; failures route to `engine.logEvalCaptureFailure` so `gbrain doctor` sees drops cross-process. **Capture is off by default** — `isEvalCaptureEnabled` resolution: explicit `config.eval.capture` (true/false) wins, else `process.env.GBRAIN_CONTRIBUTOR_MODE === '1'`, else off. Production users get a quiet brain; contributors set `export GBRAIN_CONTRIBUTOR_MODE=1` in `.zshrc` to enable the dev loop. PII scrubber gate is independent and defaults to true regardless of CONTRIBUTOR_MODE.
- `src/core/eval-capture-scrub.ts` (v0.25.0) — zero-deps PII scrubber: emails, phones, SSN, Luhn-verified credit cards, JWT-shaped tokens, bearer tokens.
- `src/core/search/hybrid.ts` — Cathedral II `Promise<SearchResult[]>` return shape unchanged in v0.25.0. Adds `onMeta?: (m: HybridSearchMeta) => void` callback so op-layer capture can record what hybridSearch actually did. Existing callers leave it undefined. **v0.33:** `HybridSearchOpts.types?: PageType[]` (defined on `SearchOpts`) threads a multi-type filter through to per-engine `searchKeyword` + `searchVector` + `searchKeywordChunks`, where it lands as `AND p.type = ANY($N::text[])`. Primary consumer is `gbrain whoknows` (filters to `['person','company']`). AND-applies alongside the existing single-value `type` filter; either or both can be used. **v0.36.3.0:** `hybridSearch` now resolves the embedding column at the boundary via `resolveColumn(loadRegistry(cfg), opts.embedding_column, cfg)` from `src/core/search/embedding-column.ts`, threads the `ResolvedColumn` descriptor into per-engine `searchVector` (not a raw string), and uses `isCacheSafe(resolved, cfg)` for the cache-skip decision (replaces the prior name-based `isDefaultColumn` check that leaked across vector spaces when a user repointed the `embedding` builtin). `cosineReScore` calls `engine.getEmbeddingsByChunkIds(ids, resolved.name)` so rerank uses vectors from the active column, not the hardcoded OpenAI `embedding`. The `query` MCP op accepts `embedding_column` for per-call A/B benchmarking; `search` (keyword-only) deliberately rejects the param. **v0.41.34.0 (retrieval-maxpool incident):** two new post-fusion stages plus the evidence stamp. `applyTitleBoost(results, query, titleBoost, floorThreshold)` (T2) multiplies a result's score by the resolved `title_boost` when `isTitlePhraseMatch` fires, stamps `title_match_boost`, and inherits the floor-ratio gate so a title match can't shove a much-stronger page below it. `applyAliasHop(engine, results, query, opts)` (T3) normalizes the query, calls `engine.resolveAliases`, and when the normalized query exactly matches a page's declared alias, surfaces that page at top-of-organic + epsilon with `alias_hit=true`. `stampEvidence(...)` (T4) runs LAST (after the alias hop, before slice) on every path — keyword-only, no-embed, and full hybrid — so MCP callers and `--explain` read the same `evidence` + `create_safety` contract. `title_boost` is resolved from the mode bundle and threaded in.
- `docs/eval-capture.md` (v0.25.0) — stable NDJSON schema reference for gbrain-evals consumers.
- `test/public-exports.test.ts` (v0.25.0 / R2) — runtime contract test. Imports each of the 17 public subpaths via package name and pins a canary symbol per module. Paired with `scripts/check-exports-count.sh`.
- `src/core/embedding.ts` — OpenAI text-embedding-3-large, batch, retry, backoff. **v0.28.7:** `BATCH_SIZE` reverted 50→100 — the original Voyage safety guard halved OpenAI throughput on every page. Per-recipe pre-split + recursive halving + adaptive shrink-on-miss now live in the gateway, so the outer paginator goes back to its original purpose: progress-callback granularity, not batch protection. **v0.41.31.0 (cost-model + stale-semantics wave):** `estimateEmbeddingCostUsd(tokens)` now prices against the CURRENTLY-CONFIGURED model's rate instead of the hardcoded OpenAI `EMBEDDING_COST_PER_1K_TOKENS`. Pre-fix, a brain on a cheaper model (e.g. ZeroEntropy) saw a `sync --all` preview that named OpenAI and over-stated spend ~2.6x. New `currentEmbeddingPricePerMTok()` resolves the per-1M-token rate via `lookupEmbeddingPrice(gatewayGetModel())` from `embedding-pricing.ts`, falling back to the OpenAI 3-large rate (0.13) only when the gateway is unconfigured (unit tests, pre-connect preview) or the model is unknown to the pricing table. `EMBEDDING_COST_PER_1K_TOKENS` is retained for back-compat with direct importers/tests. New `currentEmbeddingSignature(): string` returns the embedding-provenance signature `<provider:model>:<dims>` (e.g. `openai:text-embedding-3-large:1536`) stamped onto `pages.embedding_signature` at every embed-write site; DELIBERATELY excludes the chunker version (that's tracked separately via `pages.chunker_version`) — this signature is strictly the EMBEDDING space, so a model OR dimension swap makes the stored signature differ from the current one and a page becomes stale. Same unconfigured-gateway fallback as the cost helpers. New `willEmbedSynchronously({v2Enabled, serialFlag, noEmbed}): SyncEmbedMode` is the single source of truth for whether `gbrain sync --all` embeds at sync time (`'inline'`) or defers to per-source `embed-backfill` minion jobs (`'deferred'`) — mirrors `sync.ts`'s `effectiveNoEmbed` resolution exactly (`v2Enabled && !serialFlag && !noEmbed → deferred`) so the cost gate and the actual embed decision can never drift. New `shouldBlockSync(costUsd, floorUsd, mode): boolean` is the pure cost-gate decision: blocks ONLY when `mode === 'inline' && costUsd > floorUsd` — deferred mode never blocks (the backfill's $X/source/24h cap is the real money gate). Pinned by `test/sync-cost-preview.test.ts` + `test/embedding-signature-stale.test.ts`.
- `src/core/ai/dims.ts` (v0.33.1.1, PR #962 + #866) — per-provider `providerOptions` resolver for embed-time dimension passthrough. The single source of truth for "which provider needs which knob to produce `vector(N)`". Exports `dimsProviderOptions(implementation, modelId, dims)` (called by `embed()` in `gateway.ts`), `VOYAGE_OUTPUT_DIMENSION_MODELS` (private const — the 7 hosted Voyage models that accept `output_dimension`: `voyage-4-large`, `voyage-4`, `voyage-4-lite`, `voyage-3-large`, `voyage-3.5`, `voyage-3.5-lite`, `voyage-code-3` — nano deliberately excluded), `VOYAGE_VALID_OUTPUT_DIMS = [256, 512, 1024, 2048] as const`, `supportsVoyageOutputDimension(modelId)`, and `isValidVoyageOutputDim(dims)`. **Voyage path uses the SDK-supported `dimensions` field** (`{ openaiCompatible: { dimensions: N } }`), NOT Voyage's `output_dimension` wire-key — the existing `voyageCompatFetch` shim in `gateway.ts:541` translates `dimensions → output_dimension` before the HTTP body is built. The reverse (sending `output_dimension` from here) was the v0.33.1.0 bug class: the AI SDK's openai-compatible adapter doesn't recognize the wire-key so it was silently dropped, Voyage returned its default 1024-dim, and the gateway dimension check threw on every embed call. Runtime guard: when a Voyage flexible-dim model is configured with `dims` outside `VOYAGE_VALID_OUTPUT_DIMS`, throws `AIConfigError` with a paste-ready `gbrain config set embedding_dimensions <256|512|1024|2048>` hint at the embed boundary — fail-loud instead of opaque Voyage HTTP 400. Most common trigger: `embedding_model: voyage:voyage-4-large` configured without `embedding_dimensions` (falls back to `DEFAULT_EMBEDDING_DIMENSIONS=1536`, an OpenAI default not a Voyage one). Eva (@100yenadmin) shipped the wire-key fix in #866; Codex P3 follow-up landed the validator + valid-dims allowlist in #962.
- `src/core/ai/types.ts` — provider/recipe types. **v0.28.7 (#680):** `EmbeddingTouchpoint` extended with optional `chars_per_token` (default 4 chars/token, matching OpenAI tiktoken on English) and `safety_factor` (default 0.8, budget-utilization ceiling). Both consulted only when `max_batch_tokens` is also set. Voyage declares `chars_per_token=1` + `safety_factor=0.5` to handle dense payloads (CJK/JSON/base64) that overshoot tiktoken. The pre-split budget is `max_batch_tokens × safety_factor / chars_per_token`. **v0.28.11 (#719):** `EmbeddingTouchpoint.multimodal_models?: string[]` model-level allow-list for recipes that mix text-only + multimodal models under one touchpoint (Voyage's 12 models share `supports_multimodal: true` but only `voyage-multimodal-3` accepts `/multimodalembeddings`). When omitted, recipe-level `supports_multimodal` is sufficient. `AIGatewayConfig.embedding_multimodal_model?: string` lets `embedMultimodal()` route to a different model than `embedding_model` — brains using OpenAI for text can use Voyage for images without flipping the primary embedding pipeline. **v0.37.6.0 (#1210):** new `Recipe.default_headers?: Record<string, string>` (static) and `Recipe.resolveDefaultHeaders?(env)` (env-templated) seam for per-recipe headers that ride alongside auth on every openai-compat touchpoint. Mutually exclusive (declaring both throws `AIConfigError` at gateway-configure time); keys conflicting with the resolved auth header (`Authorization`, the resolver's custom header) are rejected at `applyResolveAuth` call time so defaults cannot accidentally shadow auth. Used by OpenRouter for the `HTTP-Referer` + `X-OpenRouter-Title` + `X-Title` attribution triple; usable by any future recipe (Together/Groq) that wants attribution.
- `src/core/ai/gateway.ts` — unified seam for every AI call. **v0.36.3.0:** `embedQuery(text, opts?)` and `isAvailable(touchpoint, modelOverride?)` accept a model override so the resolved-column path can embed via the column's provider (Voyage / ZeroEntropy / OpenAI) instead of the global default. The hybrid path passes `{embeddingModel: resolved.provider, dimensions: resolved.dimensions}`; the gateway resolves the matching recipe and routes through its `instantiateEmbedding()` branch. `isAvailable('embedding', 'voyage:voyage-3-large')` checks the override's recipe (not the default) so hybrid skips vector search only when the active column's provider is actually down — fixes the CDX-4 bug where a healthy Voyage column would skip vector retrieval because OpenAI happened to be unconfigured. **v0.35.0.0:** ZeroEntropy support lands. New `zeroEntropyCompatFetch` shim (sibling to `voyageCompatFetch`) handles ZE's non-OpenAI-compatible wire shape — rewrites the request URL from `/embeddings` to `/models/embed`, injects `input_type` (default `'document'`; `'query'` when threaded via `providerOptions.openaiCompatible.input_type`) and explicit `encoding_format: 'float'`, and rewrites the response from `{results: [{embedding}], usage: {total_bytes, total_tokens}}` to `{data: [{embedding, index}], usage: {prompt_tokens, total_tokens}}` so the SDK's openai-compatible Zod schema validates (Voyage's shim hit the same `prompt_tokens` requirement at `:655`). Layer 1 (Content-Length) + Layer 2 (per-embedding) OOM caps via a new tagged `ZeroEntropyResponseTooLargeError` class (kept separate from `VoyageResponseTooLargeError` because `test/voyage-response-cap.test.ts` does structural source-text greps pinning the Voyage name — class unification is a deferred cleanup). Wired in `instantiateEmbedding()` via the same `recipe.id === 'zeroentropyai'` branch pattern Voyage uses. New `gateway.rerank()` native HTTP path (no AI-SDK reranking abstraction): resolves the configured reranker model via `getRerankerModel()`, posts to `${recipe.base_url}/models/rerank` with bearer auth, returns `RerankResult[]` sorted by relevance score. `RerankError.reason` classifier: `auth | rate_limit | network | timeout | payload_too_large | unknown`. 5s default timeout (search hot path). Pre-flight payload guard rejects bodies over `recipe.touchpoints.reranker.max_payload_bytes` with `reason: 'payload_too_large'` so callers can fail-open without an HTTP call. `_rerankTransport` test seam mirrors `_embedTransport`. New `gateway.embedQuery(text)` companion threads `inputType: 'query'` through `dimsProviderOptions()` (now 4-arg). `getRerankerModel()` accessor + `isAvailable('reranker')` branch added. `configureGateway` + `reconfigureGatewayWithEngine` thread `reranker_model` through the same path as embedding/expansion/chat. `applyResolveAuth` + `defaultResolveAuth` widen touchpoint param to include `'reranker'`. **v0.34.1.0 (#875):** new `embedMultimodalOpenAICompat()` routes recipes with `implementation: 'openai-compatible'` (LiteLLM, Anyscale, vLLM, Gemini multimodal via proxy) through the standard `/embeddings` endpoint with content arrays carrying `image_url` entries. The pre-existing Voyage `/multimodalembeddings` path is unchanged; the gateway selects by recipe `implementation` tag. Runtime dimension validation throws `AIConfigError` (with model id + observed + expected) before the vector reaches storage when the provider returns a width that doesn't match the recipe's `default_dims` or the brain's `embedding_dimensions` config — no more cryptic `vector dimension mismatch` at INSERT time. Pinned by 11 cases in `test/openai-compat-multimodal.test.ts`. **v0.28.7 (#680):** module-scoped `_embedTransport` defaulting to AI SDK `embedMany`, with `__setEmbedTransportForTests(fn)` test seam so tests drive the public `embed()` function with a stubbed transport instead of probing private helpers. `splitByTokenBudget` and `isTokenLimitError` are now exported `@internal` — pure functions reused directly by the test file. Module-level `_shrinkState: Map<recipeId, {factor, consecutiveSuccesses}>` halves the recipe's effective `safety_factor` on token-limit miss (floor 0.05) and heals back ×1.5 toward the ceiling after `SHRINK_HEAL_AFTER=10` consecutive successes. `configureGateway()` walks every registered recipe at construction time and emits a once-per-process stderr warning for any embedding touchpoint missing `max_batch_tokens` (excluding the canonical OpenAI fast-path recipe). `resetGateway()` clears `_shrinkState`, the warned-set, and restores the real transport. ASCII flow diagram embedded in the `embed()` JSDoc covers the routing decision, recursion + halving, and shrinkState lifecycle. **v0.28.11 (#719):** `embedMultimodal()` reads `cfg.embedding_multimodal_model` first (falls back to `cfg.embedding_model` for single-model setups). After the existing recipe-level `supports_multimodal` fast-fail, validates the resolved model against `touchpoint.multimodal_models` when declared — closes the Voyage-text-only-model-into-multimodal-endpoint footgun before any HTTP call (Codex F1 from PR review). New `getMultimodalModel()` accessor mirrors `getEmbeddingModel` / `getChatModel` so doctor and integration tests can read the gateway state. **v0.33.1.1 (#962, Codex P3 follow-up):** new exported `VoyageResponseTooLargeError` tagged class at the top of the file. `voyageCompatFetch`'s two OOM-defense caps (Layer 1 Content-Length check at `:595`, Layer 2 per-embedding base64 cap at `:619`) now throw `VoyageResponseTooLargeError` instead of a generic `Error`. The inbound response-rewriter's surrounding try/catch (which intentionally swallows parse failures so misshaped Voyage responses fall through to the SDK's JSON parser) checks `instanceof VoyageResponseTooLargeError` and rethrows. Pre-fix, the Layer 2 throw was silently swallowed and the oversized response returned to the AI SDK anyway — Layer 2 was theatrical. Source-shape regression assertion in `test/voyage-response-cap.test.ts` pins the `instanceof ⇒ throw err` line.
- `src/core/ai/recipes/zeroentropyai.ts` (v0.35.0.0) — ZeroEntropy openai-compatible recipe declaring BOTH `embedding` (`zembed-1`, 7 Matryoshka dims: 2560/1280/640/320/160/80/40) AND `reranker` (`zerank-2` flagship + `zerank-1` + `zerank-1-small`, 5MB payload cap) touchpoints. `implementation: 'openai-compatible'` (NOT the misspelled `'openai-compat'` the original plan draft had — pinned by F1 regression in `test/ai/zeroentropy-recipe.test.ts`). `base_url_default: 'https://api.zeroentropy.dev/v1'` already ends with `/v1`, so the `zeroEntropyCompatFetch` URL rewrite `/embeddings → /models/embed` produces `…/v1/models/embed` (NOT `…/v1/v1/…` — pinned by F2 regression). `chars_per_token: 1` + `safety_factor: 0.5` match Voyage's dense-content hedge.
- `src/core/ai/recipes/llama-server-reranker.ts` (v0.40.6.1) — sibling of `llama-server` (the embedding recipe) for llama.cpp running in `--reranking` mode. Distinct recipe rather than dual-touchpoint extension because `--reranking` and `--embeddings` are mutually exclusive at server-launch time, so the two backends need independent base URLs (default 8081 here vs 8080 there). Declares `reranker` touchpoint with `models: []` (user-provided id matching the `--alias` the user launched llama-server with), `path: '/rerank'` (leaf-only; consumes the new `RerankerTouchpoint.path` override on the touchpoint; gateway concatenates with `base_url_default` which already ends in `/v1`, producing `…/v1/rerank` — original draft of this recipe set `path: '/v1/rerank'` which doubled the prefix, caught by post-impl `/codex review` and corrected before merge), `default_timeout_ms: 30_000` (consumed by `src/core/search/mode.ts`'s reranker timeout resolution chain — gives CPU-only first-call warmup headroom; the 5s mode-bundle default would fail-open silently as `timeout`), `cost_per_1m_tokens_usd: 0` (recognized by `FREE_LOCAL_RERANK_PROVIDERS` in `src/core/budget/budget-tracker.ts` so `--max-cost` callers don't TX2 hard-fail on local rerank). Setup hint emphasizes `--alias` because llama-server's `/v1/models` defaults model id to the gguf file path without it, which makes provider:model config strings ugly. Covers Qwen3-Reranker via llama.cpp AND self-hosted ZE weights via llama.cpp — same recipe, different `--model` at launch (quality parity with ZE-hosted NOT guaranteed; user pins their own eval). Pinned by `test/ai/recipe-llama-server-reranker.test.ts`. Voyage / Cohere / vLLM rerankers stay out of scope — different wire shapes need adapter hooks designed in a follow-up plan. Same wave (v0.40.6.1) adds: `path?: string` + `default_timeout_ms?: number` on `RerankerTouchpoint` in `src/core/ai/types.ts`; consumed by the URL build at `src/core/ai/gateway.ts:rerank()` and by mode-resolution at `src/core/search/mode.ts:resolveSearchMode` (precedence: per-call > config-key > recipe touchpoint default > mode bundle); `LLAMA_SERVER_RERANKER_BASE_URL` env passthrough in `src/cli.ts:buildGatewayConfig`; `FREE_LOCAL_RERANK_PROVIDERS` set in `src/core/budget/budget-tracker.ts:lookupPricing` (rerank-kind-only zero-pricing for the local provider prefix); doctor-fix at `src/commands/models.ts:probeRerankerConfig` to read `search.reranker.model` via `loadSearchModeConfig` + `resolveSearchMode` (closes file-plane / DB-plane divergence where doctor said "not configured" while live search was actively reranking — pre-fix bug was `getRerankerModel()` reading `GBrainConfig.reranker_model`, a file-plane field nothing writes); `probeRerankerReachability` upgraded to read the recipe's `default_timeout_ms` so CPU-only cold-start doesn't false-fail.
- `src/core/ai/recipes/openrouter.ts` (v0.37.6.0, #1210) — OpenRouter openai-compatible recipe: single key, many providers via `openrouter:<provider>/<model>` strings. `base_url_default: 'https://openrouter.ai/api/v1'`. Embedding touchpoint: `openai/text-embedding-3-small` at 1536 dims with Matryoshka `dims_options: [512, 768, 1024, 1536]` (native breakpoints from Weaviate's MRL analysis); `max_batch_tokens: 300_000` = OpenAI's aggregate-per-request token cap (NOT per-input — Codex caught the semantic in pre-merge review). Chat touchpoint declares 8 curated entry points (gpt-5.2, gpt-5.2-chat, gpt-5.5, claude-haiku-4.5, claude-sonnet-4.6, claude-opus-4.7, gemini-3-flash-preview, deepseek-chat) but openai-compat tier accepts any model ID; deliberately no `max_context_tokens` because OR's catalog spans 128K to 1M+. `supports_subagent_loop: false` is INFORMATIONAL — the real gate is `isAnthropicProvider()` in `src/core/model-config.ts` which hard-pins gbrain's subagent infra to Anthropic-direct. The recipe declares `resolveDefaultHeaders(env)` (the env-templated variant of the new `default_headers` seam) returning OR's three attribution headers: `HTTP-Referer` (required for OR to create an app-attribution entry), `X-OpenRouter-Title` (current preferred name per OR docs), `X-Title` (documented back-compat alias). Defaults to `https://gbrain.ai` / `gbrain`; forks (downstream agent deployments) override via `OPENROUTER_REFERER` / `OPENROUTER_TITLE` env vars so their traffic gets their attribution on OR's leaderboard. Smoke-tested by `test/ai/recipe-openrouter.test.ts` (11 cases including the D5 shape-test regression guard: every model in the chat list matches `^[a-z0-9-]+\/[a-z0-9._-]+$`, catching typos and malformed IDs without pinning the catalog's churn).
- `src/core/rerank-audit.ts` (v0.35.0.0) — failure-only JSONL audit at `~/.gbrain/audit/rerank-failures-YYYY-Www.jsonl` (ISO-week rotation, mirrors `src/core/audit-slug-fallback.ts`). Exports `logRerankFailure({reason, model, query_hash, doc_count, error_summary})` + `readRecentRerankFailures(days)`. **Deliberately no `logRerankSuccess`** (CDX2-F22 in plan review): writing once per tokenmax search is hot-path I/O churn AND success events leak query volume + timing into a local audit file. `gbrain doctor`'s `reranker_health` check reads `search.reranker.enabled` first so "no events in window" is interpreted correctly (disabled → ok; enabled → ok). Query text is SHA-256-prefix-hashed (8 hex chars) for privacy. `GBRAIN_AUDIT_DIR` env override honored via the shared `resolveAuditDir()`.
- `src/core/search/embedding-column.ts` (v0.36.3.0) — single source of truth for "which `content_chunks.*` column does this query rank against?" Pure functions, no engine I/O: `loadRegistry(cfg)` walks the `embedding_columns` config (DB plane, JSON map keyed by column name with `{provider, dimensions, type}` entries), seeds the OpenAI `embedding` builtin when unset, validates everything before it lands (column-name regex, type ∈ `vector | halfvec`, dims in [1, 8192], provider format) using `Object.create(null)` + `Object.hasOwn` so a key like `constructor` rejects instead of resolving to `Object.prototype.constructor`. `resolveColumn(registry, override?, cfg)` is the boundary call: returns a `ResolvedColumn` descriptor (frozen `{name, provider, dimensions, type}`) honoring per-call override → `search_embedding_column` config → `'embedding'` default. Throws `UnknownEmbeddingColumnError` with the list of registered names on miss. `isCacheSafe(resolved, cfg)` compares the full embedding SPACE (provider + dimensions + name) against cfg's default — a user who repointed the `embedding` builtin at Voyage doesn't accidentally serve OpenAI-shaped cache rows. `validateResolvedColumn(descriptor)` re-validates hand-rolled descriptors that bypass the registry (internal-SDK passthrough path) so the SQL-injection escape hatch through the descriptor field is closed. Consumed by `hybridSearch` (resolves once at the boundary, threads a `ResolvedColumn` into per-engine `searchVector` instead of a raw string), `gateway.embedQuery(text, {embeddingModel, dimensions})` (resolved column's provider drives the query-time embed call), `cosineReScore` (engine pulls vectors from the active column, not the hardcoded `embedding`), and the `query` MCP op (per-call `embedding_column` param). 538 lines of pure resolver, 511 unit cases in `test/search/embedding-column.test.ts` covering the 16 codex-flagged corners (prototype-pollution, descriptor passthrough, env-only Postgres install, empty-brain coverage gate, cache-space comparison).
- `src/core/search/rerank.ts` (v0.35.0.0) — the call-site abstraction. `applyReranker(query, results, opts)` slots between `dedupResults()` and `enforceTokenBudget()` in `src/core/search/hybrid.ts`. Slices `opts.topNIn` (default 30) by current RRF order, sends to `gateway.rerank()`, reorders by `relevanceScore` desc, and appends the un-reranked tail unchanged (recall protection). **Fail-open on every `RerankError.reason`**: any error logs via `logRerankFailure` and returns the input array unchanged. Stamps `rerank_score` onto reordered items so downstream telemetry sees the new ordering signal. `topNOut: null` is the explicit "don't truncate" signal — semantically distinct from `undefined` which means "fall through to mode bundle" (CDX2-F16). Test seam: `opts.rerankerFn` lets tests stub `gateway.rerank` without touching the network.
- `src/core/search/return-policy.ts` (v0.41.33.0, NEW — default OFF) — intent-aware adaptive return-sizing. Pure, dependency-light module that trims the final ranked candidate set to an intent-driven cap instead of always returning the full top-K (noisy) list. `entity` intent (single-answer-ish) gets a tight cap; `temporal`/`event`/`general` (enumeration-ish) get a recall-preserving cap. A `minKeep` failsafe (≥1) guarantees a human never gets a silent blank when candidates exist. WHY a cap, not a score-cliff detector: PrecisionMemBench Phase-1 instrumentation (gbrain-evals) measured that the rank1→rank2 RRF score gap is ~identical whether rank-1 is correct (0.602) or wrong (0.569) — mechanical decay, not a trustworthy separatrix; rank-1 is right in 94% of single-answer cases, so "return a tight set" is the whole win and cliff-cutting just adds noise. Exports `AdaptiveReturnConfig`, `DEFAULT_ADAPTIVE_RETURN` (frozen: `enabled=false`, `entityMax=2`, `otherMax=6`, `minKeep=1`), `AdaptiveReturnDecision` (`{applied, intent, cap, kept, total}`), `AdaptiveReturnInput` (`boolean | Partial<AdaptiveReturnConfig> | undefined`), `adaptiveReturnFromConfig(cfg)` (reads the config plane), `resolveAdaptiveReturn(perCall, fromConfig)` (defaults → config → per-call merge), `adaptiveReturnEnabled(...)` (gate check for the cache skip), and `applyAdaptiveReturn(results, intent, cfg)` (the trim). Config knobs (DB or file plane): `search.adaptive_return` (master switch, boolean), `search.adaptive_return_entity_max`, `search.adaptive_return_other_max`, `search.adaptive_return_min_keep` (each clamped to ≥1). Precision-sensitive agents tune entity=1, other=1 ≈ "return only the top result." Wired into `hybridSearch` (`src/core/search/hybrid.ts`): applied AFTER `applyReranker`, BEFORE the `limit` slice, and ONLY on the first page (`offset===0`) — paginating a confidence-gated set is incoherent, so paginated calls fall through to the fixed limit. Stamps the decision onto `HybridSearchMeta.adaptive_return` for `gbrain search --explain`. `hybridSearchCached` SKIPS the cache when the gate is on (a trimmed set must not be served to a gate-off lookup and vice versa); folding the gate params into `KNOBS_HASH` so adaptive-on calls cache safely is a v0.42+ follow-up before any mode-default flip. `SearchOpts.adaptiveReturn` + `HybridSearchMeta.adaptive_return` declared in `src/core/types.ts`. **Agent-facing surface (v0.41.33.0):** the `query` op (`src/core/operations.ts`) exposes an `adaptive_return` boolean param whose description instructs the agent WHEN to set it (single-answer questions → on; breadth/exploration → off; pass `limit:1` for a hard single-answer cap), threaded into `hybridSearchCached`. This is the path that matters — end users never touch the config knob; their agent decides per query (same pattern as `salience`/`recency`). Pinned by `test/search/return-policy.test.ts` (mechanism) + `test/search/query-op-adaptive-return.test.ts` (agent surface: param exists + description teaches both directions + the never-empty contract).
- `src/core/ai/recipes/voyage.ts` — Voyage AI openai-compatible recipe. **v0.28.7 (#680):** declares `chars_per_token=1` + `safety_factor=0.5` so the gateway pre-splits Voyage batches at a 60K-character budget (50% of 120K-token cap with the dense-tokenizer ratio). Closes the v0.27 backfill loop where ~26% of the corpus stayed un-embedded because tiktoken-grounded budgeting silently undercounted Voyage's actual token usage. **v0.28.11 (#719):** declares `multimodal_models: ['voyage-multimodal-3']` so the gateway rejects text-only Voyage models pointed at the multimodal endpoint with a clear `AIConfigError` instead of waiting for Voyage's HTTP 400. **v0.33.1.1 (#962, fixup):** recipe docstring at `:7-16` tightened to name the seven hosted flexible-dim models that accept `output_dimension` explicitly (`voyage-4-large`, `voyage-4`, `voyage-4-lite`, `voyage-3-large`, `voyage-3.5`, `voyage-3.5-lite`, `voyage-code-3`) and call out that `voyage-4-nano` is the open-weight variant listed separately by Voyage as fixed 1024-dim — does NOT accept the parameter. The "all v4 variants are flexible" misread is what caused the original PR to include nano in `VOYAGE_OUTPUT_DIMENSION_MODELS`; the negative regression assertion in `test/ai/gateway.test.ts` (`dimsProviderOptions` returns `undefined` for `voyage-4-nano`) pins the contract. **v0.37.3.0:** `voyage-code-3` is the recommended embedding model for gstack per-worktree code brains (Topology 3 in `docs/architecture/topologies.md`). Registration was already in the `models` list since pre-v0.33; the v0.37.3.0 wave adds discoverability surfaces — decision-tree branch in `docs/integrations/embedding-providers.md`, Topology 3 "Recommended embedding model" subsection, runtime nudge from `gbrain reindex --code` against non-code-tuned models. Recipe-shape regression pinned by `test/ai/voyage-code-3-recipe.test.ts`.
- `src/core/ai/recipes/anthropic.ts` — Anthropic recipe (chat + expansion touchpoints). **v0.31.12:** chat and expansion `models:` lists drop the v0.31.6 phantom `claude-sonnet-4-6-20250929` date suffix — canonical id is `claude-sonnet-4-6`. The wrong-direction alias `claude-sonnet-4-6 → claude-sonnet-4-6-20250929` is removed; a reverse alias `claude-sonnet-4-6-20250929 → claude-sonnet-4-6` keeps stale user configs working (rescues `facts.extraction_model` and `models.dream.synthesize` set by v0.31.6 installs). Recipe-shape regression pinned by `test/anthropic-model-ids.test.ts` (6 cases, verbatim cherry-pick of PR #830 plus the reverse-alias rescue case).
- `src/core/anthropic-pricing.ts` — Single source of truth for Anthropic model pricing (per-MTok input/output). **v0.31.12:** Opus 4.7 corrected from `$15/$75` to `$5/$25` (the old number was from Opus 4 generation, never refreshed when 4.7 shipped); Opus 4.6 also corrected. Consumed by `src/core/budget-meter.ts` and `src/core/cross-modal-eval/runner.ts` — the cross-modal estimator now reads `ANTHROPIC_PRICING` for Anthropic models instead of duplicating the table, killing the v0.31.6 drift bug class.
- `src/core/budget/budget-tracker.ts` (v0.37.x) — keystone primitive for the brainstorm cost-cathedral wave. One typed error (`BudgetExhausted` with `reason: 'cost' | 'runtime' | 'no_pricing'`), one schema-stable audit JSONL at `~/.gbrain/audit/budget-YYYY-Www.jsonl`. Contracts pinned by 18 unit cases: **TX1** — `record()` throws when cumulative spend exceeds cap (the cap is a real ceiling, not a suggestion); **TX2** — `reserve()` hard-fails with `reason: 'no_pricing'` when `maxCostUsd` is set AND the model is missing from pricing maps (warn-once preserved when cap is unset); **A3 amended** — `extractUsageFromError(err, fallback)` returns `err.usage` when SDK provides it, else the pessimistic fallback (caller passes `maxOutputTokens`, not the optimistic pre-call estimate). `onExhausted(cb)` callback fires once synchronously BEFORE the throw propagates so callers can persist checkpoints. Replaces three parallel copies (inline brainstorm class, cycle/budget-meter, eval-contradictions). Adapts the old `BudgetMeter` via T5 (public shape preserved + `schema_version: 1` stamped on every dream-budget audit line).
- `src/core/audit-week-file.ts` (v0.37.x, Q1) — single source of truth for ISO-week audit JSONL filename math. Exports `isoWeek(d)`, `isoWeekFilename(prefix, now?)`, `resolveAuditDir()` (honors `GBRAIN_AUDIT_DIR`). Year-boundary correctness pinned by tests at 2020-W53 (the 53-week year), 2025-W01 rolling in from 2024-12-30 (Monday), 2026-W01. Four call sites migrated in T4: `src/core/minions/handlers/shell-audit.ts`, `src/core/facts/phantom-audit.ts`, `src/core/audit-slug-fallback.ts`, `src/core/cycle/budget-meter.ts`. Each call site keeps its `compute<X>AuditFilename` thin wrapper for back-compat with existing tests.
- `src/core/ai/gateway.ts:withBudgetTracker` (v0.37.x, T3 / TX5) — gateway-layer enforcement via `AsyncLocalStorage<BudgetTracker>`. `withBudgetTracker(tracker, fn)` installs the tracker on the module-internal store; every `gateway.chat / embed / rerank` call inside the scope auto-composes (reserve before, record in try/finally). Outside-scope calls are budget no-ops (current behavior preserved). Nested scopes restore the outer tracker on exit. `getCurrentBudgetTracker()` is the test seam. The chat path uses A3-amended pessimistic fallback on error paths; the embed path estimates input tokens from char count × recipe's `chars_per_token` because the AI SDK doesn't surface per-batch embed token usage; the rerank path estimates char count of query+docs. 6 unit cases pin the contract.
- `src/core/diarize/payload-fitter.ts` (v0.37.x, P6 / Q3) — generic fit-arbitrarily-large-items-into-per-call-token-budget utility. `'batch'` strategy is deterministic token-budgeted chunking with no LLM calls. `'summarize'` strategy embed-clusters into ceil(items/4) groups via cheap deterministic nearest-neighbor on cosine, Haiku-summarizes each cluster via `Promise.allSettled` at parallelism=4 (Perf1). Each Haiku call composes the active BudgetTracker via T3's AsyncLocalStorage. The quality gate (codex outside-voice finding #4): when `success_ratio < min_success_ratio` (default 0.75), result is flagged `degraded: true` — the fitter preserves the successful subset; the caller decides whether to surface a partial result or abort.
- `src/core/brainstorm/checkpoint.ts` (v0.37.x, P7 / TX3+TX4+A5 amended) — crash-resilient checkpoint for `gbrain brainstorm` and `gbrain lsd`. Persists FULL idea bodies (~50KB per run) so resume can MERGE the pre-crash ideas with the post-resume ideas before the judge runs (codex's load-bearing finding — a resume that produces only second-run output is silent partial output). `run_id = sha256(question + profile + sort(close_slugs) + sort(far_slugs)).slice(0,16)` — NO embedding bits, stable across embedding-model swaps. Atomic write via `.tmp + rename`. ONE resume flag (`--resume <run_id>` — the proposed `--retry-failed` was dropped per TX4: failed AND never-attempted crosses both go through `--resume`). `--list-runs` prints saved run_ids mtime-newest-first. `--force-resume` bypasses the 7-day staleness gate. The cycle purge phase (`gbrain dream --phase purge`) GCs checkpoints older than 7 days via `gcStaleCheckpoints(7)`. Pinned by 20 unit cases + 3 E2E cases in `test/e2e/brainstorm-resume.test.ts` including the load-bearing merge contract.
- `src/core/remediation-checkpoint.ts` (v0.37.x, T7 / A4 amended) — `doctor --remediate` checkpoint at `~/.gbrain/remediation/<plan_hash>.json`. `plan_hash = sha256(JSON.stringify(sorted recommendation ids)).slice(0,16)`. Schema-versioned. Atomic write via `.tmp + rename`. `gbrain doctor --remediate --resume <plan_hash>` (or with no arg — picks the newest matching checkpoint) loads it and skips already-completed steps. Mismatched plan_hash refuses with a paste-ready message. Cleared on clean completion. Pinned by 13 unit cases.
- `src/core/model-config.ts` — Model-string resolution (the seam every internal LLM call walks through). **v0.31.12:** four-tier system (`ModelTier = 'utility' | 'reasoning' | 'deep' | 'subagent'`) with `TIER_DEFAULTS` (utility→haiku-4-5, reasoning→sonnet-4-6, deep→opus-4-7, subagent→sonnet-4-6) and `tier?: ModelTier` on `ResolveModelOpts`. Resolution chain is now 8 steps: cliFlag → deprecated key → config key → `models.default` → `models.tier.<tier>` → env var → `TIER_DEFAULTS[tier]` → caller fallback. Two new exports — `isAnthropicProvider(modelString)` checks `provider:model` prefix OR `claude-` bare-id pattern, and `enforceSubagentAnthropic()` is the layer-2 runtime guard: when `tier === 'subagent'` resolves to a non-Anthropic provider, it emits a once-per-`(source, model)` stderr warn AND falls back to `TIER_DEFAULTS.subagent` instead of letting the Anthropic Messages API tool-loop attempt to run on OpenAI/Gemini. `_resetDeprecationWarningsForTest()` now also clears `_subagentTierWarningsEmitted` so tests re-emit. **v0.41.21.0:** `isAnthropicProvider` routes through the new `splitProviderModelId` from `src/core/model-id.ts` so slash-form ids (`anthropic/claude-sonnet-4-6`) classify correctly. Pre-fix the colon-only check silently returned false on slash form, so a user who set `models.tier.subagent` to the slash form had `enforceSubagentAnthropic` fall through to `TIER_DEFAULTS.subagent` AND skipped the warn — the explicit config was honored as if it had never been set. Now both shapes classify the same. Pinned by 2 new cases in `test/model-config.serial.test.ts`.
- `src/core/ai/model-resolver.ts` — Recipe-touchpoint validator. **v0.31.12:** `assertTouchpoint(recipe, touchpoint, modelId, extendedModels?)` gains an optional 4th `extendedModels: ReadonlySet<string>` argument. When the modelId is in that set, the native-recipe allowlist throw is bypassed — the user explicitly opted into this model via config so we let provider rejection surface as `model_not_found` at HTTP call time (and `gbrain models doctor` catches it earlier). Default code paths with hardcoded model strings MUST NOT pass `extendedModels` — typos in source code still fail fast. Replaces the earlier plan to soften the validator wholesale (Codex F4/F5 in plan review flagged that as too broad — it would have removed the fail-fast contract for chat + expand + embed all three).
- `src/core/ai/gateway.ts` extension (v0.31.12) — new module-scoped `_extendedModels: Map<providerId, Set<modelId>>` registry feeds `assertTouchpoint`'s 4th-arg path. New `reconfigureGatewayWithEngine(engine)` async function is called from `cli.ts` after `engine.connect()` (and before every command except `CLI_ONLY` no-DB commands) — re-resolves expansion + chat defaults through `resolveModel()` so `models.tier.*` and `models.default` overrides apply to expansion + chat both. `DEFAULT_CHAT_MODEL` corrected to `anthropic:claude-sonnet-4-6` (was the v0.31.6 phantom `-20250929`). New `__setChatTransportForTests` seam mirrors `__setEmbedTransportForTests` so tests drive `chat()` with a stubbed transport.
- `src/core/minions/queue.ts` extension (v0.31.12) — `MinionQueue.add()` now rejects `subagent` jobs whose `data.model` resolves through `isAnthropicProvider()` to a non-Anthropic provider. Lazy-imports `model-config.ts` to avoid pulling engine types into queue's eager-load surface. Layer 1 of the three-layer subagent provider enforcement (Codex F1+F2 in plan review). Layers 2 + 3 live in `src/core/model-config.ts` (`enforceSubagentAnthropic` runtime fallback) and `src/commands/doctor.ts` (`subagent_provider` check). Pinned by 3 cases in `test/agent-cli.test.ts`.
- `src/commands/models.ts` (v0.31.12) — `gbrain models [--json]` read-only routing dashboard: prints tier defaults (`utility`/`reasoning`/`deep`/`subagent`), the resolved value for each (re-walking the resolution chain to attribute properly), every per-task override (11 `PER_TASK_KEYS` entries — `models.dream.synthesize`, `models.dream.patterns`, `models.drift`, `models.auto_think`, `models.think`, `models.subagent`, `facts.extraction_model`, `models.eval.longmemeval`, `models.expansion`, `models.chat`, `models.dream.synthesize_verdict`), the alias map (defaults + user overrides), and a source-of-truth column showing `default` / `config: <key>` / `env: <VAR>`. `gbrain models doctor [--skip=<provider>] [--json]` fires a 1-token `gateway.chat()` probe against each configured chat + expansion model and classifies failures into `{model_not_found, auth, rate_limit, network, unknown}` — the structural fix for the v0.31.6 silent-no-op bug class. Wired into `cli.ts` dispatch table + `CLI_ONLY` set. **v0.33.1.1 (#962, Codex P3 follow-up):** doctor gains a zero-token `embedding_config` probe that runs FIRST, before any chat/expansion probes spend money. `probeEmbeddingConfig()` reads `getEmbeddingModel()` + `getEmbeddingDimensions()` from the gateway, parses the model id, and (for Voyage flexible-dim models) checks `isValidVoyageOutputDim(dims)` against `VOYAGE_VALID_OUTPUT_DIMS`. New `ProbeStatus` variant `'config'` and optional `fix?: string` field on `ProbeResult` — surfaced in both human output (paste-ready `gbrain config set ...` line under the bad probe) and JSON output. New touchpoint label `'embedding_config'` joins `'chat'` and `'expansion'` in the probe-row taxonomy. Closes the Voyage flexible-dim bug class at config time, not first-embed.
- `src/commands/doctor.ts` extension (v0.31.12) — new `subagent_provider` check (layer 3 of 3 — Codex F13). Warns when `models.tier.subagent` is explicitly set to a non-Anthropic provider (fail-loud since the user clearly meant it — message names the bad value and prints the paste-ready fix command `gbrain config set models.tier.subagent anthropic:claude-sonnet-4-6`); also warns when `models.default` would sneak `subagent` into a non-Anthropic provider via tier inheritance. OK status when subagent tier resolves to Anthropic. Tests cover all three paths in `test/doctor.test.ts`.
- `src/core/skill-trigger-index.ts` (v0.41.14.0, closes #1451) — Shared loader that unions per-skill SKILL.md frontmatter `triggers:` with curated RESOLVER.md / AGENTS.md rows from `skillsDir` AND the parent directory (preserves the OpenClaw workspace-root layout). UNION semantics: explicit RESOLVER.md rows ADD to frontmatter triggers (don't replace). Dedup keyed on `(skillPath, trigger.trim().toLowerCase())` so case/whitespace drift collapses to one entry. Three consumers fold through this primitive — `checkResolvable`, `runRoutingEvalCli`, `mounts-cache.composeResolvers` — closing the v0.41 drift bug class (#1451) where per-consumer loaders meant fixing frontmatter for doctor wouldn't reach the routing-eval CLI or cross-brain composed dispatchers. Exports `loadSkillTriggerIndex(skillsDir): SkillTriggerEntry[]`, `entriesToResolverContent(entries): string` (synthesizes a markdown-table resolver-content string for `runRoutingEval`'s string-content API), `findPrimaryResolverPath(skillsDir): string | null`, plus the `FRONTMATTER_SECTION` constant and `_resetWarnedSkillsForTests` test seam. Skip rules: non-directory entries, `_*` / `.*` prefixes, `conventions/` + `migrations/` subdirs, skills with no `SKILL.md` (deprecated `install/` graceful-skipped), skills with no `triggers:` array, malformed YAML (warn-once + skip). Reuses `parseSkillFrontmatter` from `src/core/skill-frontmatter.ts` (regex-based, not full YAML — adequate for the uniform shape every bundled skill uses, follow-up TODO if drift surfaces). Pinned by 18 hermetic cases in `test/skill-trigger-index.test.ts` covering frontmatter auto-registration, RESOLVER.md/AGENTS.md merge, OpenClaw `../AGENTS.md` parent-dir scan, case-insensitive dedupe, deprecated `install` skip, missing-skillsDir resilience, malformed-frontmatter warn-once, and `entriesToResolverContent` round-trip through `parseResolverEntries`. CI gate: `bun run check:resolver` (= `bun src/cli.ts check-resolvable --strict --skills-dir skills/`) wired into `bun run verify` so future drift between frontmatter and routing-eval fixtures fails PR CI.
- `src/core/skill-catalog.ts` (v0.41.36.0, PR1) — host-repo skill catalog backing the MCP `list_skills` / `get_skill` ops. Lets a thin MCP client (Codex desktop, Claude Code, Claude Cowork, Perplexity) DISCOVER + FOLLOW the agent repo's fat-markdown skills over `gbrain serve` — a skill is prose, not code, so "using" one = fetching its body then calling the same gbrain MCP tools the server already exposes. Read-scope, NOT localOnly (defensible only via the full mitigation stack documented in the file's trust-boundary memo). Mitigations: (1) **publish gate** — `assertPublishEnabled(ctx, publishSkills)`; remote callers require `mcp.publish_skills === true`, default-OFF at runtime so an upgrade never silently grants existing read tokens host-skill read; local callers (`ctx.remote === false`) always pass. (2) **path confinement** — `assertSkillNameShape` rejects separators/`..`/null/space before any FS access; the client `name` is a manifest LOOKUP KEY (via `loadOrDeriveManifest`), never a raw path segment; `confineManifestPath` does realpath + relative-containment + `SKILL.md`-regular-file check on EVERY entry (defeats poisoned manifest.json `path`, symlink/`..` escape). (3) **frontmatter allowlist** — `GetSkillResult.frontmatter` projects a safe subset; private `writes_to` (brain taxonomy) + `sources` (absolute paths) dropped. (4) **prose-only + 256KB cap** (`MAX_SKILL_MD_BYTES`, env `GBRAIN_MAX_SKILL_MD_BYTES`) — no source code (tarballs deferred to PR2), size-checked twice (statSync + UTF-8 byte length). (5) **no install_path serve for remote** — remote callers use `autoDetectSkillsDir` (no install-path tier) so a hosted gbrain with no agent repo returns `storage_error`, never gbrain's own bundled dev skills; local callers use `autoDetectSkillsDirReadOnly`. (6) MCP rate-limiter caps call rate. Config reads honor BOTH planes: `readMcpPublishSkills` / `readMcpSkillsDir` prefer the DB plane (`engine.getConfig`, what `gbrain config set` + `gbrain init` write) over the file plane (`ctx.config.mcp`). D7 tool-honesty: `crossReferenceTools(declared, ctx)` splits a skill's declared `tools:` into `usable_tools` (in this server's op set AND callable by the caller's scope) vs `unavailable_tools`, and `buildSkillCatalog`'s `instructions` envelope (`SKILL_CATALOG_INSTRUCTIONS` from operations-descriptions.ts) carries the load-bearing "these are prose, follow-then-call-tools" use protocol. Skills are host-filesystem repo-global — `sourceScopeOpts(ctx)` / `ctx.brainId` deliberately do NOT apply (one server host = one skills dir = one catalog). `buildSkillCatalog` is resilient (one malformed/escaping skill is skipped, never throws the call). Config keys land in `src/core/config.ts`: `GBrainConfig.mcp?: { publish_skills?, skills_dir? }` + `KNOWN_CONFIG_KEYS` entries `mcp.publish_skills` / `mcp.publish_skills_prompted` / `mcp.skills_dir` + the `mcp.` prefix in `KNOWN_CONFIG_KEY_PREFIXES`. `src/commands/init.ts` writes `config.mcp = { publish_skills: true, ... }` for new PGLite + Postgres installs (existing config wins on re-init so a prior opt-out survives). `src/commands/upgrade.ts:runPostUpgrade` adds a one-time consent prompt (gated by `mcp.publish_skills_prompted`; existing installs stay OFF until the owner opts in; TTY readline Y/n with non-TTY paste-ready hint). The two ops register in `src/core/operations.ts` (`list_skills` with optional `section` filter + `cliHints: { name: 'skills' }`; `get_skill` taking `name` + `cliHints: { name: 'skill', positional: ['name'] }`) and dynamically import this module to avoid the import cycle (skill-catalog statically imports the `operations` array for D7). Descriptions + envelopes in `src/core/operations-descriptions.ts` (`LIST_SKILLS_DESCRIPTION`, `GET_SKILL_DESCRIPTION`, `SKILL_CATALOG_INSTRUCTIONS`, `SKILL_CLIENT_GUIDANCE`), pinned by `test/operations-descriptions.test.ts`. CLI surfaces: `gbrain skills` / `gbrain skill <name>` (via cliHints). Pinned by `test/skill-catalog.test.ts`, `test/skill-catalog-security.test.ts` (path-confinement / poisoned-manifest / symlink-escape), `test/skill-catalog-transports.test.ts` (publish-gate + remote-vs-local resolution) over fixtures at `test/fixtures/skill-catalog/`. PR2 (downloadable/installable skillpack tarballs) is deferred and tracked in TODOS.md.
- `src/core/check-resolvable.ts` — Resolver validation: reachability, MECE overlap, DRY checks, structured fix objects. v0.14.1: `CROSS_CUTTING_PATTERNS.conventions` is an array (notability gate accepts both `conventions/quality.md` and `_brain-filing-rules.md`). New `extractDelegationTargets()` parses `> **Convention:**`, `> **Filing rule:**`, and inline backtick references. DRY suppression is proximity-based via `DRY_PROXIMITY_LINES = 40`. **v0.41.7.0:** `parseResolverEntries` accepts a second compact list format alongside the original markdown table (`- **skill-name**: trigger1 | trigger2 | trigger3` or `- skill-name: trigger1 | trigger2`). Both shapes can mix in one file; the v0.31.7 multi-resolver merge folds them into one entry stream. Skill name MUST be kebab-lowercase (regex `[a-z][a-z0-9-]+`) so prose bullets like `- **Note**: …`, `- **Convention**: …`, `- **TODO**: …` in real-world AGENTS.md files don't false-match as skill rows (codex F2 / D4). `skillPath` is ALWAYS derived as `skills/<name>/SKILL.md`: an optional `→ \`skills/path\`` (or ASCII `->`) suffix is stripped from the trigger string but NOT honored as the path — two downstream consumers (`routing-eval.ts:skillSlugFromPath`, the manifest lookup at `:367`) assume the convention, and honoring the explicit path would silently break their coverage. For non-conventional paths, use the table format. Multi-trigger rows fan out to one entry per trigger sharing the same `skillPath`; `checkResolvable` dedupes downstream so the reachability count counts each skill once. Closes the OpenClaw bug class where a 306-skill agent's list-format resolver registered 238 FAILs ("skill not reachable from RESOLVER.md") on every `gbrain doctor` run — productionized from upstream PR #1370 by @garrytan-agents. Pinned by 11 new unit cases in `test/check-resolvable.test.ts` (bold + plain forms, Unicode + ASCII suffix strip, ellipsis filter, empty pipe segments, mixed shapes, prose-bullet rejection regression) and the 8-case integration suite in `test/check-resolvable-openclaw-compact.test.ts` over two fixtures: `test/fixtures/openclaw-compact-resolver/` (10 skills in pure compact form) + `test/fixtures/openclaw-mixed-merge/` (table-format `skills/RESOLVER.md` + compact `../AGENTS.md` for the v0.31.7 merge contract). User-facing tutorial: `docs/guides/scaling-skills.md` walks through when and why to switch to the compact format (the three-tier scaling architecture that gets a 300-skill agent down to ~4K tokens per turn from ~25K with zero capability loss).
- `src/core/repo-root.ts` — Shared `findRepoRoot(startDir?)` (v0.16.4): walks up from `startDir` (default `process.cwd()`) looking for `skills/RESOLVER.md`. Zero-dependency module imported by both `doctor.ts` and `check-resolvable.ts`. Parameterized `startDir` makes tests hermetic. **v0.31.7:** read-path / write-path split. `autoDetectSkillsDir` (shared, read+write-safe) gains tier-0 `$GBRAIN_SKILLS_DIR` explicit operator override (Docker mounts, CI, monorepo subdirs) ahead of the existing 4-tier chain. New `autoDetectSkillsDirReadOnly` wraps it with a tier-5 install-path fallback that walks up from `fileURLToPath(import.meta.url)` and gates on `isGbrainRepoRoot` so unrelated repos can't false-positive. Read-path callers (`doctor`, `check-resolvable`, `routing-eval`) use the read-only variant; write-path callers (`skillpack install`, `skillify scaffold`, `post-install-advisory`) deliberately stay on the shared function so `gbrain skillpack install` from `~` cannot silently retarget the bundled gbrain repo's `skills/` instead of the user's actual workspace. Two new `SkillsDirSource` variants: `'env_explicit'`, `'install_path'`. New `AUTO_DETECT_HINT_READ_ONLY` documents the extra tier. The D6 `--fix` safety gate in `doctor.ts` + `check-resolvable.ts` refuses auto-repair when `detected.source === 'install_path'` so `gbrain doctor --fix` from `~` cannot silently rewrite the bundled install tree.
- `src/commands/check-resolvable.ts` — Standalone CLI wrapper (v0.16.4) over `checkResolvable()`. Exports `parseFlags`, `resolveSkillsDir`, `DEFERRED`, `runCheckResolvable`. Exit rule: **1 on any issue (warnings OR errors)**, stricter than doctor's `ok` flag — honors README:259. Stable JSON envelope `{ok, skillsDir, report, autoFix, deferred, error, message}` — same shape on success and error paths. `--fix` path runs `autoFixDryViolations` BEFORE `checkResolvable` (same ordering as doctor). `scripts/skillify-check.ts` subprocess-calls `gbrain check-resolvable --json` (cached per process) and fails loud on binary-missing — no silent false-pass. **v0.19:** AGENTS.md workspaces now resolve natively (see `src/core/resolver-filenames.ts`) — gbrain inspects the 107-skill OpenClaw deployment whether the routing file is `RESOLVER.md` or `AGENTS.md`. `DEFERRED[]` is empty — Checks 5 + 6 shipped as real code, not issue URLs. **v0.31.7:** the resolver lookup switched from first-match-wins to the multi-file merge in `src/core/check-resolvable.ts` — entries collected from every `RESOLVER.md` / `AGENTS.md` across the skills dir AND its parent, deduped by `skillPath` (first occurrence wins). Lifted reachable skills on the reference OpenClaw layout from 37/224 to 200/224 — the deployment ships a thin `skills/RESOLVER.md` (~40 entries from skillpack) plus a fat `../AGENTS.md` (200+ entries, the real dispatcher), and the previous code only saw the first one. The CLI also switched to `autoDetectSkillsDirReadOnly` so `cd ~ && gbrain check-resolvable` finds the bundled skills via the install-path fallback. `--fix` carries the same D6 safety gate as `gbrain doctor --fix`: refuses to write when `detected.source === 'install_path'`.
- `src/core/resolver-filenames.ts` (v0.19) — central list of accepted routing filenames (`RESOLVER.md`, `AGENTS.md`). Shared by `findRepoRoot`, `check-resolvable`, and skillpack install so every code path walks the same fallback chain.
- `src/commands/skillify.ts` + `src/core/skillify/{generator,templates}.ts` (v0.19) — `gbrain skillify scaffold <name>` creates all stubs for a new skill in one command: SKILL.md, script, tests, routing-eval.jsonl, resolver entry, filing-rules pointer. `gbrain skillify check <script>` runs the 10-step checklist (LLM evals, routing evals, check-resolvable gate, filing audit) against a candidate skill before it lands.
- `src/commands/skillify-check.ts` (v0.19) — `gbrain skillpack-check` agent-readable health report. Exit 0/1/2 for CI pipeline gating; JSON for debugging. Wraps `check-resolvable --json`, `doctor --json`, and migration ledger into one payload so agents can decide whether a human action is required. **v0.37.1.0:** required item 12 (`brain_first_compliance`) joins the 11-item checklist. Calls `analyzeSkillBrainFirst()` on the candidate SKILL.md; exits 1 when the verdict is `missing_brain_first` (external-lookup pattern present, no callout, no `brain_first: exempt`). The corresponding scaffold path in `src/core/skillify/templates.ts` pre-inserts the canonical Convention callout into new SKILL.md files so freshly-scaffolded skills pass item 12 by default.
- `src/commands/book-mirror.ts` (v0.25.1) — `gbrain book-mirror --chapters-dir <path> --slug <slug> [flags]`. Flagship of the v0.25.1 skills wave. Submits N read-only subagent jobs (one per chapter; `allowed_tools: ['get_page', 'search']`), waits for all via `waitForCompletion`, reads each child's `job.result`, assembles two-column markdown CLI-side, writes a single operator-trust `put_page` to `media/books/<slug>-personalized.md`. Codex HIGH-1 fix applied: trust narrowing happens at the tool-allowlist layer (subagents can't call put_page) instead of allowedSlugPrefixes — untrusted EPUB content cannot prompt-inject any people page. Cost-estimate prompt before launching; refuses to spend in non-TTY without `--yes`. Per-chapter idempotency keys (`book-mirror:<slug>:ch-<N>`) for retry-friendly re-runs. Partial-failure handling: assembles with completed chapters and a `## Failed chapters` section listing retries. Test surface: `test/book-mirror.test.ts` (9 cases — CLI registration + source invariants).
- `src/commands/skillpack.ts` + `src/core/skillpack/{bundle,scaffold,reference,migrate-fence,scrub-legacy,harvest,harvest-lint,copy,apply-hunks,diff-text,installer}.ts` (v0.19 → v0.36) — **v0.36 contract change**: managed-block install model retired. `install` and `uninstall` removed (clean break, no alias; both exit non-zero with a hint pointing at the replacement command). New surface: `scaffold` (one-time additive copy via shared `copyArtifacts` helper in `copy.ts`; refuses to overwrite existing files; partial-state fills missing paired sources declared in SKILL.md frontmatter `sources:`), `reference` (read-only diff lens with agent-readable framing line + `--apply-clean-hunks` two-way auto-apply via pure-JS unified-diff parser/applier in `apply-hunks.ts` + `diff-text.ts`), `migrate-fence` (one-shot strip of legacy fence; cumulative-slugs receipt → row-parsing fallback; preserves rows verbatim as user-owned routing), `scrub-legacy-fence-rows` (opt-in row cleanup with skill-present + non-empty-triggers gate), `harvest` (host→gbrain inverse with symlink-reject + canonical-path containment via `validateUploadPath`-style gate + default-on privacy linter in `harvest-lint.ts` against `~/.gbrain/harvest-private-patterns.txt` plus built-in `\bWintermute\b` + email + Slack-channel patterns; rollback on match). Paired-source declarations moved from `openclaw.plugin.json` to each SKILL.md's frontmatter `sources:` array (D2; validated by `loadSkillSources` in `bundle.ts`). `autoDetectSkillsDir` (in `src/core/repo-root.ts`) gains a `cwd_walk_up` tier ahead of `~/.openclaw/workspace` (D3; non-OpenClaw hosts like `~/git/wintermute` auto-detect; R5 regression preserves `$OPENCLAW_WORKSPACE` precedence). `gbrain skillpack check --strict` exits non-zero on drift (CI gate); top-level `gbrain skillpack-check` keeps exit-1-on-issues for cron compat. Companion editorial skill `skills/skillpack-harvest/SKILL.md` drives the genericization checklist before the CLI runs. Design + workflow doc: `docs/guides/skillpacks-as-scaffolding.md`. ~600 LOC of managed-block machinery deleted; ~400 LOC of new modules + ~1000 LOC of new test coverage across `test/skillpack-{copy,scaffold,reference,reference-apply,apply-hunks,migrate-fence,scrub-legacy,harvest,harvest-lint,frontmatter-sources}.test.ts` + 9-case E2E in `test/e2e/skillpack-flow.test.ts`. `installer.ts` + `test/skillpack-install.test.ts` survive for now — `gbrain skillpack diff` still uses `diffSkill` from there; slated for v0.37 cleanup. **Historical (v0.19-v0.35.1):** managed-block model with `<!-- gbrain:skillpack:begin -->`/`end -->` fence, `cumulative-slugs="..."` receipt, content-hash gates, lockfile; `install --all` prune; `uninstall` with D8 receipt gate + D11 atomic-refusal content-hash pre-scan. Replaced wholesale in v0.36.
- `src/core/skillpack/{manifest-v1,tarball,state,remote-source,trust-prompt,bootstrap-display,scaffold-third-party,registry-schema,registry-client,rubric,doctor,init-scaffold,pack-publish,endorse,audit}.ts` + `examples/skillpack-reference/` + `docs/skillpack-anatomy.md` + `scripts/build-skillpack-anatomy.ts` (v0.37.0.0) — third-party skillpack ecosystem layered on the v0.36 scaffolding contract. `gbrain skillpack scaffold <owner/repo|https-url|./tgz|./local-dir>` resolves the spec via `classifySpec`, fetches through SSRF-hardened `git-remote.ts` (git) or extracts the tarball into `~/.gbrain/skillpack-cache/<host>/<owner>/<repo>/<sha>/`, validates `skillpack.json` (api_version `gbrain-skillpack-v1`), checks `gbrain_min_version`, surfaces a TOFU first-install identity-confirm prompt (codex G4: author + source + pinned commit + tarball SHA + tier; non-TTY requires `--trust`), records the pin in machine-owned `~/.gbrain/skillpack-state.json` (codex G1; schema `gbrain-skillpack-state-v1`, atomic `.tmp + rename`, `isAlreadyTrusted` skips re-prompt on author+pin match), runs through the existing `enumerateScaffoldEntries` → `copyArtifacts` pipeline (one-time additive copy; refuses to overwrite), then DISPLAYS `runbooks/bootstrap.md` without executing (codex T1 npm-postinstall lesson — "gbrain deliberately does NOT auto-execute these steps"). Registry catalog at `garrytan/gbrain-skillpack-registry` (separate repo) split into `registry.json` (PR-able, schema `gbrain-registry-v1`) + `endorsements.json` (Garry-only overlay, `gbrain-endorsements-v1`); `effectiveTier` merges. `registry-client.ts` fetches both URLs via `If-None-Match` etag with 1h soft-TTL + stale-fallback (origins: `fresh_fetch | cache_warm | cache_soft_stale | cache_hard_stale`); hard-fail only on no-cache + no-network. `gbrain skillpack {search,info,registry,doctor,init,pack,endorse}` CLI surface. Doctor walks `SKILLPACK_RUBRIC_V1` (10 binary dimensions, codex T4 split into 5 required CORE — manifest_valid, skills_have_skill_md, routing_evals_present ≥5 intents, skills_have_unique_triggers MECE, changelog_present_and_current — and 5 quality BADGES — unit_tests_present, e2e_tests_present, llm_eval_present ≥3 cases, bootstrap_runbook_present, license_present); tier eligibility: `endorsed` needs all 10, `community` needs core + ≥3 badges, `experimental` needs core only, `blocked` when any core fails. `--quick` ~5s structural sweep; `--fix --yes` auto-scaffolds `auto_fixable: true` dimensions and refuses to overwrite files whose mtime is newer than `skillpack.json`. `gbrain skillpack init <name>` lands the full cathedral (11 files: skillpack.json, SKILL.md, routing-eval.jsonl, test/example.test.ts, e2e/example.e2e.test.ts, evals/example.judge.json, runbooks/{bootstrap,uninstall,upgrade-template}.md, CHANGELOG, README, LICENSE); freshly-init'd pack scores 10/10. `--minimal` skips test/e2e/evals. `gbrain skillpack pack` packs a deterministic tarball via GNU tar (`--sort=name --mtime=@0 --owner=0 --group=0 --numeric-owner` + `GZIP=-n` + `TZ=UTC`); refuses on `tier_eligibility === 'blocked'`. Extract caps (5000 files / 100MB total / 1MB per file / 255-char paths / 100:1 compression ratio); rejects symlinks/hardlinks/devices/FIFOs. `gbrain skillpack endorse <name> [--tier ...] [--push] [--dry-run]` runs in a clone of the registry repo: validates pack exists in `registry.json`, mutates `endorsements.json` via pure `applyEndorsement`, stable-key-orders the write, stages + commits `endorse: <name> -> <tier>`, optionally pushes. JSONL audit at `~/.gbrain/audit/skillpack-YYYY-Www.jsonl` (ISO-week rotated, honors `GBRAIN_AUDIT_DIR`). `examples/skillpack-reference/` is a real 10/10 reference pack pinned by `test/e2e/skillpack-third-party.test.ts`. `docs/skillpack-anatomy.md` is auto-generated via `scripts/build-skillpack-anatomy.ts` with `--check` mode for CI drift detection. CLI dispatch in `src/commands/skillpack.ts` disambiguates third-party (contains `/`, `://`, `.tgz`) from bundled-skill kebab; kebab routes bundled-first, registry-fallback. Test coverage: `test/skillpack-{manifest-v1,tarball,state,remote-source,trust-prompt,registry-schema,registry-client,rubric,doctor,init-scaffold,pack-publish,endorse,audit,scaffold-third-party}.test.ts` + e2e at `test/e2e/skillpack-third-party.test.ts`. Plan + spec at `docs/designs/SKILLPACK_REGISTRY_V1_SPEC.md`. Deferred to follow-up waves: subprocess sandbox for publish-gate, `garrytan/gbrain-skillpack-registry` repo creation + CI workflow split (codex G3), Printing Press cross-list at `mvanhorn/printing-press-library`, generated `gbrain-cli` via Printing Press, W4.5 retrofit of ~25 bundled skills to 10/10.
- `src/core/archive-crawler-config.ts` (v0.25.1) — D12 + codex HIGH-4 safety gate for the `archive-crawler` skill. Refuses to run unless `archive-crawler.scan_paths:` is explicitly set in the brain repo's `gbrain.yml`. Mirrors the storage-config.ts parsing pattern (sibling file; separate concern from storage tiering). `loadArchiveCrawlerConfig(repoPath)` throws `ArchiveCrawlerConfigError(missing_section | empty_scan_paths | invalid_path | parse_error)`. `normalizeAndValidateArchiveCrawlerConfig` rejects relative paths and `..` traversal; `~` is expanded; trailing-slash normalized for unambiguous prefix matching. `isPathAllowed(candidate, config)` is the runtime per-file gate (scan_paths prefix-match with directory-boundary correctness; deny_paths overrides). Tests in `test/archive-crawler-config.test.ts` (19 cases).
- `test/helpers/cli-pty-runner.ts` (v0.25.1) — generic real-PTY harness ported from gstack and trimmed to ~470 lines. Uses pure `Bun.spawn({terminal:})` (Bun 1.3.10+; engines.bun pin in package.json). Generic primitives only — no plan-mode orchestrators. Exports: `launchPty`, `resolveBinary`, `stripAnsi`, `parseNumberedOptions`, `optionsSignature`, `isNumberedOptionListVisible`, `isTrustDialogVisible`. Self-tests in `test/cli-pty-runner.test.ts` (24 cases).
- `src/core/skill-manifest.ts` (v0.19) — parser for `skill-manifest.json` records. Used by skillpack installer to detect drift between the shipped bundle and the user's local edits, so updates merge instead of overwriting.
- `src/commands/routing-eval.ts` + `src/core/routing-eval.ts` (v0.19) — `gbrain routing-eval` catches user phrasings that route to the wrong skill. Reads `skills/<name>/routing-eval.jsonl` fixtures (`{intent, expected_skill, ambiguous_with?}`). Structural layer runs in `check-resolvable` by default (zero API cost). The `--llm` flag is accepted as a placeholder for a future LLM tie-break layer; in v0.24.0 it emits a stderr notice and runs structural only. False positives surface before users hit them. **v0.31.7:** switched to `autoDetectSkillsDirReadOnly` and the same multi-file resolver merge as `check-resolvable`, so on OpenClaw layouts (`skills/RESOLVER.md` + `../AGENTS.md`) all three commands see the same trigger index — previously `routing-eval` read only the first resolver file it found. The v0.25.1 wave skills' RESOLVER.md rows were also synced to include the full frontmatter `triggers:` arrays (was only the first trigger), so the structural matcher actually sees the realistic phrasings; ambiguous-fixture annotations cover deliberate skill chains like `enrich → article-enrichment`.
- `src/core/filing-audit.ts` + `skills/_brain-filing-rules.json` (v0.19) — Check 6 of `check-resolvable`. Parses new `writes_pages:` / `writes_to:` frontmatter on skills and audits their filing claims against the filing-rules JSON. Warning-only in v0.19, upgrades to error in v0.20. **v0.37.1.0:** internal `parseFrontmatter` reduced to a thin wrapper over the new shared `src/core/skill-frontmatter.ts` parser so both filing-audit and skill-brain-first read the same shape (`tools?`, `triggers?`, `brain_first?: 'exempt'`, typed `brain_first_typo`) from one source of truth.
- `src/core/skill-frontmatter.ts` (v0.37.1.0) — shared content-based SKILL.md frontmatter parser. Replaces filing-audit's private path-based parser. Recognizes the new `brain_first: 'exempt'` declarative opt-out and surfaces near-miss declarations (`brain-first`, `BrainFirst`, quoted values, unknown values) as a typed `brain_first_typo` field so doctor can emit a paste-ready hint rather than fail silently. Single canonical form: snake_case `brain_first: exempt`, lowercase, unquoted.
- `src/core/skill-brain-first.ts` (v0.37.1.0) — pure analyzer. `analyzeSkillBrainFirst(skillPath, content): SkillBrainFirstResult` walks the compliance ladder for every SKILL.md: (1) absent external-lookup pattern → `no_external`; (2) `brain_first: exempt` frontmatter → `exempt_frontmatter`; (3) canonical `> **Convention:** see [conventions/brain-first.md](...)` callout → `compliant_callout`; (4) explicit `## Phase 1: Brain` heading → `compliant_phase`; (5) first `gbrain search` / `query` / `get_page` reference precedes first external pattern in the BODY (frontmatter stripped) → `compliant_position`; (6) else `missing_brain_first` warn. External pattern set: word-boundary regex over `web_search`, `web_fetch`, `exa`, `perplexity`, `happenstance`, `crustdata`, `captain_api`, `firecrawl`. Position scan is BODY-ONLY (A4) so a `tools: [web_search]` frontmatter declaration doesn't false-flag the skill. PR #1206's 40-name `EXEMPT_SKILLS` list is preserved as `FORMERLY_HARDCODED_EXEMPT` purely so doctor can emit a "this used to be auto-exempt, declare `brain_first: exempt` if still appropriate" hint (CMT1). Consumed by 3 surfaces: doctor check, skillify-check item 12, dry-fix MISSING_RULE_PATTERNS.
- `src/core/skill-fix-gates.ts` (v0.37.1.0) — shared safety primitives extracted from `dry-fix.ts`. `getWorkingTreeStatus(file)` 3-state (`'clean' | 'dirty' | 'not_a_repo'`); `isInsideCodeFence(content, offset)`; `findAfterH1Paragraph(content)` (canonical insertion offset for the auto-inserted Convention callout). Both REPLACE expanders (existing v0.14.1 DRY violations) and the new INSERT expander (MISSING_RULE_PATTERNS) consume from here so the install-path D6 refusal and dirty-tree gates apply uniformly. `src/core/dry-fix.ts` re-exports for back-compat with existing call sites.
- `src/core/audit-skill-brain-first.ts` (v0.37.1.0) — snapshot+diff JSONL audit at `~/.gbrain/audit/skill-brain-first-YYYY-Www.jsonl` (ISO-week rotated, honors `GBRAIN_AUDIT_DIR` via the shared `resolveAuditDir()`). `recordBrainFirstRun(results)` reads the previous snapshot at `~/.gbrain/audit/skill-brain-first-snapshot.json`, diffs against the current results, writes transition events (`detected | resolved | fixed`) one line per change, then atomically overwrites the snapshot via `.tmp + rename`. **Transition-only writes** — a stable brain produces 0 audit lines per doctor run, so `tail -20` shows real signal instead of noise. `readRecentBrainFirstEvents(days)` is the readback path used by the future `skill_brain_first_trend` doctor check (filed in TODOS.md). Snapshot file is last-writer-wins under concurrent doctor runs; subsequent runs reconcile.
- `src/core/dry-fix.ts` — `gbrain doctor --fix` engine. `autoFixDryViolations(fixes, {dryRun})` rewrites inlined rules to `> **Convention:** see [path](path).` callouts via three shape-aware expanders (bullet / blockquote / paragraph). Five guards: working-tree-dirty (`getWorkingTreeStatus()` returns 3-state `'clean' | 'dirty' | 'not_a_repo'`), no-git-backup, inside-code-fence, already-delegated (40-line proximity, consistent with detector), ambiguous-multi-match, block-is-callout. `execFileSync` array args (no shell — no injection surface). EOF newline preserved. **v0.37.1.0:** safety primitives extracted to `src/core/skill-fix-gates.ts` (back-compat re-exports preserved). New `MISSING_RULE_PATTERNS` INSERT pattern type lives alongside the existing REPLACE patterns — same auto-fix entry point, same git-safety gates, but instead of rewriting an existing block, INSERT patterns place a canonical callout at a target offset (today: `after-h1-paragraph` only; designed to extend). The first INSERT pattern is `brain_first`, which auto-inserts `> **Convention:** see [conventions/brain-first.md](../conventions/brain-first.md) for the lookup chain (search → query → get_page → external).` on any flagged SKILL.md whose analyzer verdict is `missing_brain_first`. Idempotent — re-runs detect the existing callout and skip.
- `src/core/backoff.ts` — Adaptive load-aware throttling: CPU/memory checks, exponential backoff, active hours multiplier
- `src/core/retry.ts` (v0.41.19.0, extended v0.41.27.0) — canonical retry primitive for transient connection errors. Exports `withRetry<T>(fn, opts)` execution wrapper + `BULK_RETRY_OPTS` constant (`{maxRetries:3, delayMs:1000, delayMaxMs:10000, jitter:'decorrelated'}`) tuned for Supabase Supavisor's 5-10s circuit-breaker recovery window + `BATCH_AUDIT_SITES` typed const (closed enum of every audit-emission site) + `resolveBulkRetryOpts(env)` (reads `GBRAIN_BULK_MAX_RETRIES` / `GBRAIN_BULK_RETRY_BASE_MS` / `GBRAIN_BULK_RETRY_MAX_MS` with `>=0` validation, throws on bad input with paste-ready hint) + `abortableSleep(ms, signal?)` (AbortSignal-aware setTimeout) + `RetryAbortError` (tagged error for clean shutdown) + `computeNextDelay()` (pure-fn for 3 jitter modes: `'none'`, `'full'`, `'decorrelated'`). The execution wrapper is consumed by `postgres-engine.ts` + `pglite-engine.ts` batch primitives (`addLinksBatch` / `addTimelineEntriesBatch` / `upsertChunks`) so every caller — current AND future — inherits retry as part of the data-primitive's contract. CI guard `scripts/check-no-double-retry.sh` fails the build on `withRetry(...engine.batch...)` patterns (prevents 3×3=9 retry amplification). CI guard `scripts/check-batch-audit-site.sh` validates every string-literal `auditSite: '...'` against the closed `BATCH_AUDIT_SITES` enum. **Closes the v0.41.17 production incident** where ~3,000 rows were silently lost per dream cycle on a 16K-page brain because the prior single-500ms-retry shape couldn't survive Supavisor's 5-10s circuit-breaker recovery. Decorrelated jitter (AWS-style: `uniform(base, prevDelay*3)` capped at `delayMaxMs`) replaces naive `'full'` jitter which allowed near-zero retries that re-hit the still-recovering breaker. Pinned by `test/core/retry.test.ts` (37 cases) + `test/core/retry-stress.slow.test.ts` (5 cases simulating 100 batches × 30% blip rate, asserts zero row loss). **v0.41.27.0 (#1570):** `WithRetryOpts` gains optional `reconnect?: () => Promise<void>` callback awaited in the catch branch AFTER `isRetryableConnError` classification but BEFORE the inter-attempt sleep — lets engine-level callers rebuild a dead pool/singleton between attempts. `PostgresEngine.batchRetry` injects `() => this.reconnect()` so the v0.22.1 race-safe `_reconnecting` guard kicks in transparently. Fail-loud posture (per codex outside-voice finding 3): a reconnect throw PROPAGATES as the new error, replacing the symptomatic "No database connection" so operators see the real cause (auth failure, EHOSTUNREACH). `onRetry` callbacks now also awaited (back-compat-safe: existing sync arrows work identically; async callbacks now correctly delay the sleep). Pinned by `test/core/retry-reconnect.test.ts` (5 cases: ordering, back-compat, fail-loud propagation, signal-abort short-circuit, awaited onRetry timing) + `test/e2e/db-singleton-shared-recovery.test.ts` (3 DB-gated cases pinning shared-singleton survival via retry reconnect + diagnostic audit fires on disconnect + instance-pool disconnect doesn't touch module singleton).
- `src/core/audit/batch-retry-audit.ts` (v0.41.19.0, extended v0.41.26.1) — JSONL audit primitive for batch-retry events. Built on `audit-writer.ts` cathedral. Schema: `{ts, site, batch_size, attempt, outcome: 'success' | 'exhausted', delay_ms, error_message_summary, error_code?}`. Privacy posture: NEVER logs slugs / page IDs / content (mirrors `shell-audit.ts` from v0.20+). `logBatchRetry` fires per successful retry recovery; `logBatchExhausted` fires when retries exhaust and rows are lost. `readRecentBatchRetryEvents(hours=24)` returns `{events, corrupted_lines, files_scanned, files_unreadable}` — corruption + permission errors surface to doctor, not silently swallowed (codex H-9). `pruneOldBatchRetryAuditFiles(daysToKeep=30)` deletes old files (codex H-8 — implements the v0.41 plan's "30-day pruning convention" for real). Called from `gbrain dream --phase purge`. File: `~/.gbrain/audit/batch-retry-YYYY-Www.jsonl` (honors `GBRAIN_AUDIT_DIR`). **v0.41.26.1 privacy backfill:** `summarizeError` now routes error messages through the shared `redactConnectionInfo` helper from `src/core/audit/redact-connection-info.ts` BEFORE truncation, so DSNs / hostnames / credentials / IPv4 octets can't leak from a Postgres connection-failure error into operator-shared JSONL dumps. Same risk class as lock-renewal-audit; closed in the same wave. Pinned by `test/audit/batch-retry-audit.test.ts` (12 cases) + new `test/audit/batch-retry-redaction.test.ts` (3 privacy regressions).
- `src/core/audit/lock-renewal-audit.ts` (v0.41.26.1) — JSONL audit primitive for per-job lock-renewal faults. Sibling of `batch-retry-audit.ts`; built on `audit-writer.ts`. Four outcomes: `failure` (single renewLock throw, counter incremented), `success_after_failure` (recovery; emits the recovery count), `gave_up` (time-based deadline exceeded; abort fired), `executeJob_rejected` (the SECOND unhandledRejection vector from D7 — the stored `executeJob(...).finally(...)` promise itself rejected, e.g. failJob threw during the same DB outage). Schema: `{ts, job_id, job_name, attempt?, outcome, error_message_summary?, error_code?}`. Privacy: NEVER logs `lock_token` or `job.data`. Error summaries route through `redactConnectionInfo` BEFORE truncation. Defense-in-depth: every audit call inside the lock-renewal tick's catch block is wrapped in its own inner try/catch so a misbehaving audit-writer can't re-introduce the unhandledRejection bug class via a new surface. `readRecentLockRenewalEvents(hours=24)` walks current + previous ISO week with corrupted-line tolerance. `pruneOldLockRenewalAuditFiles(daysToKeep=30)` is ready for future dream-cycle purge wiring (filed as TODO-LR-3). File: `~/.gbrain/audit/lock-renewal-YYYY-Www.jsonl`. Operator UX is `tail -F` until the doctor check lands (TODO-LR-2). Pinned by `test/audit/lock-renewal-audit.test.ts` (11 cases).
- `src/core/audit/redact-connection-info.ts` (v0.41.26.1) — Shared pure helper. `redactConnectionInfo(text: string): string` strips Postgres connection info before any audit JSONL write: `postgres://`/`postgresql://` URLs, `host=foo`, `user=foo`, `password=foo`, `pwd=foo`, IPv4 octets. Each match becomes `<REDACTED:kind>`. Negative-lookbehind/lookahead `[\w.@-]` on the IPv4 pattern defeats version-string false positives like `v3.1.4.0` or `tree-sitter@0.26.3.1` while still matching real IPs in PG errors (`(192.168.1.42)`). Order-sensitive pattern set: URL forms first so substrings inside URLs don't get double-redacted. Idempotent (running twice produces same output), pure (no I/O), hot-path-safe (regex compiled at module load). Wired into BOTH `lock-renewal-audit.ts` (new) AND `batch-retry-audit.ts` (privacy backfill — same risk class). Risk model documented in module header: Postgres errors during connection failures embed DSNs / credentials / hostnames into error messages; operators routinely paste audit dumps into GitHub issues / Slack to debug; the audit channel must be safe to share by construction. Known limitations: bare-quoted hostnames (`at "db.example.com"`) and bare-quoted usernames (`for user "postgres.foo"`) are NOT caught — the IP in those PG error shapes is the highest-value leak and IS caught. Quoted-string patterns filed as TODO-LR-5. Pinned by `test/audit/redact-connection-info.test.ts` (15 cases covering all 5 patterns + real Supabase fixture + ENOTFOUND fixture + version-string false-positive defense).
- `src/core/minions/lock-renewal-tick.ts` (v0.41.26.1) — Pure extracted function from `MinionWorker.launchJob`'s setInterval body. The structural fix that closes the v0.41.22.1 production unhandledRejection crash class. Exports `runLockRenewalTick(deps, state) → Promise<TickResult>` plus `resolveLockRenewalKnobs(env, lockDuration) → LockRenewalKnobs`. Three env knobs all parsed as positive integers with stderr-warn-once-per-process on bad input + default fallback: `GBRAIN_LOCK_RENEWAL_MAX_FAILURES` (default 3, audit-labeling only — abort triggering uses time-based instead), `GBRAIN_LOCK_RENEWAL_CALL_TIMEOUT_MS` (default `lockDuration/3`, bounds the hung-renewLock vector via `Promise.race`), `GBRAIN_LOCK_RENEWAL_SAFETY_MARGIN_MS` (default `lockDuration/6`, ensures we release before stall-detector reclaim). The tick checks `state.cancelled()` at three guard points (entry, after await resolves, after await throws) so a long renewLock that resolves after the job ended bails cleanly. Result type is a tagged union `{kind: 'ok' | 'cancelled' | 'lock_lost' | 'should_abort', reason?}` that the worker switches on; all `abort.abort()` / `clearInterval` side effects live in the worker's closure scope, not the pure function. Audit calls wrapped in inner try/catch (codex C4 defense-in-depth) so the audit module can never re-introduce the bug class through a new surface. Pinned by `test/worker-lock-renewal.test.ts` (18 hermetic state-machine cases — no fs, no PGLite, no real setInterval).
- `scripts/check-worker-lock-renewal-shape.sh` (v0.41.26.1, D4) — CI guard wired into `bun run verify`. Two invariants on `src/core/minions/worker.ts`: (1) the v0.41.22.1 bug pattern `lockTimer = setInterval(async ...)` must NOT appear (narrowed via `lockTimer =` prefix so unrelated `setInterval(async)` calls elsewhere in the file — like the stall detector at line ~269, codex C13 territory — don't false-fire), (2) `runLockRenewalTick` must remain referenced so the pure-function test seam survives refactors. Bug-pattern-specific by design (codex C12) — a future refactor to `setTimeout`-recursion or `AbortController`-based scheduling passes as long as the bug pattern stays absent. Uses POSIX ERE + `[[:space:]]` for BSD-grep portability. Honors `GBRAIN_LOCK_RENEWAL_SHAPE_TARGET` env override for fixture-based meta-tests. Pinned by `test/scripts/check-worker-lock-renewal-shape.test.ts` (5 cases including the C13 false-positive defense for the stall-detector pattern elsewhere in the file).
- `src/commands/doctor.ts:checkBatchRetryHealth` (v0.41.19.0, extended v0.41.27.0) — `batch_retry_health` check surfacing Supavisor circuit-breaker incidents. Wired into both `runDoctor` (local) and `doctorReportRemote` (thin-client). Reads last **24h** (not 7d — codex H-9: avoid permanent noise from one historical blip). States: `ok` (zero exhausted in 24h OR <3 from a single site), `warn` (>=3 same-site OR >=5 cross-site), `fail` (>=20 sustained breaker). Surfaces bad `GBRAIN_BULK_*` env at doctor startup (codex M-10) instead of first-retry. Corrupt-JSONL tolerant. Paste-ready fix hints in every warn/fail message. Pinned by `test/doctor-batch-retry.test.ts` (10 cases). **v0.41.27.0 (#1570, codex finding 11):** extended (NOT a new check) to read `readRecentDbDisconnects(24)` and append `Disconnect-call audit: N call(s) in 24h (most recent caller: <frame>).` to ALL three message paths (ok / warn / fail). The single-place surface keeps connection-incident signal greppable from one `gbrain doctor --json` call so operators correlating the v0.41.27 retry-reconnect symptom fix with the offending caller don't have to grep two audit files. Module-import wrapped in try/catch so older brains without the v0.41.27 audit file degrade silently.
- `src/core/audit/db-disconnect-audit.ts` (v0.41.27.0, #1570, NEW) — JSONL audit for every call to `db.disconnect()` and `PostgresEngine.disconnect()`. Built on `audit-writer.ts` cathedral (no parallel subsystem; codex finding 11). Schema: `{ts, engine_kind: 'postgres'|'pglite'|'unknown', connection_style: 'module'|'instance'|'unknown', caller_stack, command, pid}`. `caller_stack` captured via `new Error().stack` truncated to ~20 frames so operators identify the offending caller without inflating JSONL forever. Privacy: stack frames carry file paths but NO SQL content / row data / user strings — matches the v0.20 shell-audit posture. File: `~/.gbrain/audit/db-disconnect-YYYY-Www.jsonl` (honors `GBRAIN_AUDIT_DIR`). `readRecentDbDisconnects(hours=24)` walks current + previous ISO week and returns `{count, most_recent_caller, files_scanned}`. **The instrument half of the "instrument first, fix later" pivot** — v0.41.27.0 ships the symptom fix (retry reconnect callback + facts:absorb drain) AND this diagnostic surface; v0.41.28+ patches the specific ownership boundary once production data tells us which code path is calling `disconnect()` mid-process. Wired into `src/core/db.ts:disconnect` and `src/core/postgres-engine.ts:disconnect` (logs BEFORE the early-return branches so even no-op disconnects on never-connected engines are recorded — that case may itself be a caller-side bug). Pinned by `test/db-disconnect-audit.test.ts` (6 cases: round-trip, stack truncation, sort order, empty-dir nulls, stable feature name, EROFS best-effort).
- `src/core/facts/queue.ts:FactsQueue.drainPending` (v0.41.27.0, #1570) — new method `drainPending({timeout?: number}): Promise<{drained, unfinished}>`. Semantically distinct from `shutdown()` (which calls `this.internalAbort.abort()` and would abort the very facts:absorb worker trying to log its post-completion event — preserving the bug class we're fixing per codex finding 9). Drain lets in-flight finish; only the wait is bounded. Default timeout `1000ms` so commands that don't enqueue facts pay only one fast 0ms check before exit (per codex finding 10). `src/cli.ts` op-dispatch finally block awaits `getFactsQueue().drainPending({timeout: 1000})` BEFORE `engine.disconnect()`. Lazy-import keeps the facts-queue module off the hot path for ops that never touch it. Closes the trailing `'No database connection'` line that fired on stderr after `gbrain capture` because the post-page-write facts:absorb queued work outlived the CLI process. Pinned by `test/facts-queue-drain-pending.test.ts` (4 cases: empty fast-path, in-flight settled without abort, unfinished count on timeout, default timeout = 1000ms).
- `scripts/check-no-double-retry.sh` + `scripts/check-batch-audit-site.sh` (v0.41.19.0) — CI lint guards wired into `bun run verify`. The former greps src/ for `withRetry(...engine.{addLinksBatch|addTimelineEntriesBatch|upsertChunks})` patterns and fails the build on hit (Eng-D6 migration ordering hazard — prevents 3×3=9 retry amplification on incomplete reverts). The latter extracts every string-literal `auditSite: '...'` from src/ and validates each appears in the `BATCH_AUDIT_SITES` const in `src/core/retry.ts` (codex H-7 typo guard — prevents fragmented doctor output).
- `src/core/fail-improve.ts` — Deterministic-first, LLM-fallback loop with JSONL failure logging and auto-test generation
- `src/core/transcription.ts` — Audio transcription: Groq Whisper (default), OpenAI fallback, ffmpeg segmentation for >25MB
- `src/core/enrichment-service.ts` — Global enrichment service: entity slug generation, tier auto-escalation, batch throttling
- `src/core/data-research.ts` — Recipe validation, field extraction (MRR/ARR regex), dedup, tracker parsing, HTML stripping
- `src/commands/embed.ts` — `gbrain embed [--stale|--all] [--slugs ...]`. v0.22.1 (#409, contributed by @atrevino47): `--stale` path now starts with `engine.countStaleChunks()` (single SELECT count(*) WHERE embedding IS NULL, ~50 bytes wire). On a fully-embedded brain that's a 1-line short-circuit — no further reads. When stale chunks exist, `engine.listStaleChunks()` returns just the chunks needing embeddings (slug + chunk_index + chunk_text + metadata, no `vector(1536)` payload). Caller groups by slug, embeds via OpenAI, re-upserts via `upsertChunks`. Replaces the prior page-walk that pulled every chunk's embedding column over the wire and discarded most. **v0.40.3.0:** all 16 `console.log` / `console.error` call sites migrated to `slog` / `serr` from `src/core/console-prefix.ts` so that when `runEmbedCore` runs inside a per-source `withSourcePrefix` scope (which the `gbrain sync --all` worker pool installs), every line carries the `[<source-id>] ` prefix. Standalone `gbrain embed --stale` callers see identical output to v0.40.2 because slog/serr fall through to bare console fns outside the wrap. **v0.41.31.0:** every embed-write path now stamps `pages.embedding_signature` via `engine.setPageEmbeddingSignature(slug, {sourceId, signature: currentEmbeddingSignature()})` so a later model/dims swap is detectable as stale. The per-slug path (`embedPage`, used by `gbrain embed <slug>` AND sync's post-import embed step) and the full-re-embed path (`embedAll`) stamp unconditionally per page. The stale path (`embedAllStale`) first calls `invalidateStaleSignatureEmbeddings` on a live run so signature-drifted pages flow through the NULL cursor, then stamps each page — but ONLY when EVERY chunk was stale this pass (a partially-stale page keeps preserved chunks of unknown provenance, so it stays unstamped rather than falsely marked current; `embed --all` fully re-embeds + stamps those). dry-run never mutates: it counts signature-drift via the widened `countStaleChunks({signature})` predicate without NULLing anything.
- `src/core/conversation-parser/` (v0.41.16.0, v0.41.24.0, v0.41.29.0) — 14-pattern built-in chat-format registry + opt-in LLM polish/fallback. Replaces the single inline regex that PR #1461 was trying to extend with one more shape. **v0.41.29.0** added the 14th pattern `bold-name-no-time` (regex `/^\*\*(?!\[)(.+?):\*\*\s*(.*)$/`, declared at index 3 after `bold-paren-time`): parses `**Speaker:** text` with NO per-line timestamp — the shape Circleback / Granola / Zoom emit. Anchors every message at `T00:00:00Z` of the frontmatter date (no fabricated wall-clock; line order preserves sequence), same no-time convention as `irc-classic`. The non-shadow guarantee is the colon-INSIDE-bold regex (NOT declaration order — `parse.ts` scores every candidate independently, order is only the tie-break); the `(?!\[)` lookahead rejects telegram-bracket `**[18:37] Name:**` so disabling telegram-bracket yields an honest `no_match` instead of `speaker="[18:37] Name"`. Because `**Label:** text` is a common prose idiom, the pattern sets the new optional `PatternEntry.score_full_body: true`: `parse.ts` recomputes the winner's acceptance score over the FULL body (not just the 10-line head window) before the `SCORING_MIN_ACCEPTANCE` floor, so a notes page with bold labels clustered in its first 10 lines (head score 0.3, which is NOT `< SCORING_HEAD_TRIGGER_THRESHOLD` so the head fallback never fires) drops to its true low density and stays `no_match` instead of mis-parsing as a conversation. The same wave scrubbed the pre-existing real names in `bold-paren-time`'s `test_positive`. Pinned by the `bold-name-no-time` + clustered-head `no_match` cases in `test/conversation-parser/parse.test.ts` + `bold-name-no-time.jsonl` / `adversarial.jsonl` fixtures. **v0.41.24.0 (closes #1533)** added the 13th pattern `bold-paren-time` (`**Speaker** (HH:MM): text` and `**Speaker** (HH:MM:SS): text` — the time-only shape an OpenClaw meeting-ingestion pipeline produces from Circleback transcripts; date_source: frontmatter) AND tightened the parser's fallback gates in `parse.ts`: `SCORING_HEAD_TRIGGER_THRESHOLD = 0.3` triggers a full-body re-score when the head pass scores below that (closes the bug class where a stray head match at 0.1 — e.g. blockquote that accidentally matches an unrelated pattern — suppressed the fallback entirely); `SCORING_MIN_ACCEPTANCE = 0.05` blocks essay false-positives (a 300-line essay with one stray chat-shape line scores ~0.003, below the floor, stays `no_match` instead of returning a 1-message regex_match). Both gates pinned by 11 new unit cases in `test/conversation-parser/parse.test.ts`. New exported `scorePatternFull(body, entry)` for direct full-body scoring; private `getNonBlankLines(body, headCap?)` + `scoreFromLines(lines, entry)` helpers DRY the quick_reject+regex loop. Empirical against all Circleback meetings in `~/git/brain/meetings/`: 113 of 367 parse correctly post-fix (was 0); 20,167 messages flow through to the fact extractor (was 0). The other 254 are notes-only meetings whose transcripts live in separate files. Plan + Codex absorption at `~/.claude/plans/system-instruction-you-are-working-starry-frost.md`. Modules: `types.ts` (PatternEntry + ParseResult + DateContext + CaptureMap + TimezonePolicy), `builtins.ts` (13 hand-vetted patterns sourced from public format docs — iMessage/Slack, Telegram bracket + text-export, bold-paren-time, Discord classic + export, WhatsApp ISO + US, Signal, Matrix/Element, IRC classic + weechat, Teams export; module-load validation runs every `test_positive[]` + `test_negative[]` sample at startup, so a typo in any built-in regex makes gbrain refuse to start; `DEFAULT_SPEAKER_CLEAN` exported as the PR #1461 helper promoted to a module-level default), `parse.ts` (orchestrator with D18 pattern-priority scoring across the first 10 lines + D8 date derivation chain `explicit > frontmatter.date > effective_date > '1970-01-01'` + D5 multi-line continuation + D19 timezone warning), `llm-base.ts` (shared `runLlmCall<T>` with content-hash cache in-process + DB-persistent via migration v97 + 4-strategy JSON repair + Anthropic-key probe; both polish and fallback are thin wrappers per D6 DRY), `llm-polish.ts` (per D15 opt-IN; headroom guard skips when tracker within $0.10 of cap; pure `applyPolish` for merge/drop/edit ops), `llm-fallback.ts` (per D15 opt-IN; per D17 NO regex inference + NO persistence — silent corruption avoided), `eval.ts` (`scoreFixture` + `aggregateScores` + `parseFixtureJsonl` for the fixture-corpus CI gate), `nightly-probe.ts` (DI-stubbed; mode-gated default per D10 — tokenmax=ON, conservative/balanced opt-in; adversarial false-positive detection). CLI surfaces at `src/commands/eval-conversation-parser.ts` (`gbrain eval conversation-parser <fixture.jsonl>` exit 0/1/2 — wired into `bun run verify` via `check:conversation-parser`) and `src/commands/conversation-parser.ts` (`scan <slug>` for debug, `list-builtins` for operator discoverability, `validate <file>` emits "deferred to v0.42+" notice). Doctor checks: `conversation_format_coverage` (per-pattern hit count + unmatched %), `progressive_batch_audit_health` (abort-verdict counts from last 7d), `conversation_parser_probe_health` (opt-in nightly probe state). Closes PR #1461 — contributor's `BRACKET_TIME_RX` + `cleanSpeaker` survive verbatim as the `telegram-bracket` built-in + `DEFAULT_SPEAKER_CLEAN` export, Co-Authored-By preserved. Plan + 23 decisions + codex outside-voice absorption at `~/.claude/plans/system-instruction-you-are-working-cuddly-hollerith.md`. Pinned by 74 unit cases across `test/conversation-parser/{parse,llm-base,llm-fallback,llm-polish,nightly-probe}.test.ts` + the 27-case PR #1461 baseline at `test/extract-conversation-facts.test.ts` (back-compat invariant). Migration v97 (`conversation_parser_llm_cache_table`). Fixtures at `test/fixtures/conversation-formats/{imessage,telegram-bracket,whatsapp-iso,whatsapp-us,signal-export,irc-classic,irc-weechat,matrix-element,teams-export,all,adversarial}.jsonl` with `scripts/check-fixture-privacy.sh` banning real-name leaks.
- `src/core/progressive-batch/` (v0.41.16.0) — shared ramp-up + cost-cap + verification primitive extracted after rule-of-three was comfortably past (12+ ad-hoc cost-prompt patterns scattered across reindex, reindex-multimodal, book-mirror, brainstorm, eval-suspected-contradictions, post-upgrade-reembed, eval-contradictions/cost-prompt). Wintermute-inspired ramp shape (trial 10 → ramp 100 → ramp 500 → full with verification at each stage), productionized as a runtime primitive with verifier+policy injection (callers describe HOW TO MEASURE SUCCESS, not WHEN TO WAIT FOR CTRL-C). Modules: `types.ts` (Stage, StageVerdict, AbortReason, discriminated `Verifier` union per D20: `OutputCountVerifier | IdempotentMutationVerifier | NoopVerifier`, Policy, StageReport), `orchestrator.ts` (`runProgressiveBatch(items, verifier, policy, runner)` — reads `getCurrentBudgetTracker()` ahead of `Policy.maxCostUsd` per D3 fail-closed; null both ways triggers `abort_cost_cap reason='no_budget_safety_net'`), `audit.ts` (ISO-week JSONL at `~/.gbrain/audit/progressive-batch-YYYY-Www.jsonl` via the shared `audit-writer` primitive), `stage-report.ts` (ASCII stage-report formatter for the default `Policy.onStageReport` handler). Env knobs: `GBRAIN_PROGRESSIVE_BATCH_DISABLED=1` (skip ramp + stderr warn), `GBRAIN_PROGRESSIVE_BATCH_AUTO=1` (skip Ctrl-C grace), `GBRAIN_PROGRESSIVE_BATCH_STAGES=10,100,500` (override). v0.41.16.0 ships with ONE proven consumer (the parser cathedral via extract-conversation-facts retrofit); the 9-site retrofit of `reindex.ts`, `reindex-multimodal.ts`, `reindex-code.ts`, `post-upgrade-reembed.ts`, `book-mirror.ts`, `brainstorm/orchestrator.ts`, `eval-suspected-contradictions.ts`, `eval-contradictions/cost-prompt.ts`, `contextual-reindex-per-chunk.ts` lands as the v0.41.14.0+ follow-up wave per D2's bisectability requirement (each retrofit gets its own commit; behavior parity tested before/after migration). Per D21: sites that previously "jumped straight to full" keep doing so by default; ramp is opt-in per-site via `Policy.interactiveAbortMs > 0`. Pinned by 35 unit cases in `test/progressive-batch/orchestrator.test.ts` covering every verdict path.
- `src/commands/extract-conversation-facts.ts` + `src/core/cycle/conversation-facts-backfill.ts` (v0.41.11.0) — bulk fact extraction for long-form conversation pages. The recall-miss class on long iMessage/Slack imports (60K+ msg history; a chunk that reads only "Locker 93 code 9494" has no topical anchor because "cabin" was established 50K messages earlier) gets fixed by walking conversation/meeting/slack/email pages, splitting into time-windowed segments (30-min gap or 30-msg cap), prepending a topical/temporal header ("Conversation between A and B from <iso1> to <iso2>"), and running through the existing `extractFactsFromTurn()` so the resulting anchor-rich facts surface in `gbrain search` (which already blends facts). Architecture decisions absorbed from 2 Codex outside-voice rounds + 2 eng review passes: **strict per-source core** (`runExtractConversationFactsCore({sourceId, ...})` always takes one sourceId; CLI + cycle phase each do their own multi-source iteration because PHASE_SCOPE='source' is taxonomy-only per cycle.ts:131); **two-phase enumeration** (paginated `listPages({type, sourceId, limit:10})` so worst case is 10×25MB=250MB resident vs PR #1406's unbounded; per-page body cap MAX_PAGE_BODY_BYTES=25MB with `pages_skipped_too_large` counter surfaced in doctor); **page-global row_num accumulator** (facts unique index is `(source_id, source_markdown_slug, row_num)` per migration v51 — per-segment row_num would collide on segment 2); **page-level TERMINAL audit row** written to facts table after all segments commit (source='cli:extract-conversation-facts:terminal'; doctor's NOT EXISTS query matches the terminal row, NOT any-fact-for-slug, so partial-extraction pages stay in backlog); **optional `opts.budgetTracker?`** (when present, core uses it as-is — nested `withBudgetTracker` REPLACES per gateway.ts:2011; when absent, core auto-wraps with `BudgetTracker({maxCostUsd})`); **body read covers compiled_truth + timeline** (iMessage importers put history in timeline half; PR's `compiled_truth ?? ''` would silently drop it); **honors `facts.extraction_enabled` kill-switch** with `--override-disabled` escape; **--types LIST allowlist** (`conversation,meeting,slack,email`) with CLI default reading `cycle.conversation_facts_backfill.types` config as single source of truth; **fingerprint on sourceId only** so widening types config doesn't invalidate completed-page state; **string-encoded op-checkpoint** entries `"<sourceId>|<slug>|<endIso>"` for resume only (op_checkpoints stores string[] and is 7-day GC'd — durable audit is the facts table itself via terminal row); **`--background` via maybeBackground** (Minion handler `extract-conversation-facts` re-creates BudgetTracker from `data.max_cost_usd`; on `BudgetExhausted` mid-job, catches + persists + marks `completed` with `result.budget_exhausted=true` — NOT a failure). The companion cycle phase `conversation_facts_backfill` (default OFF; `gbrain config set cycle.conversation_facts_backfill.enabled true` opts in) iterates `listSources(engine)` directly, creates ONE brain-wide tracker per tick + wraps the loop in `withBudgetTracker` + passes the tracker into every per-source invocation via `opts.budgetTracker` so the core doesn't nest-replace. Two-layer cost AND walltime protection: per-source caps (`max_cost_usd=$1`, `max_walltime_min=20`) AND brain-wide caps (`max_total_cost_usd=$5`, `max_total_walltime_min=30`). Pinned by 27 unit cases in `test/extract-conversation-facts.test.ts` (parse/segment/render/checkpoint/fingerprint/terminal-audit/row_num/F2-kill-switch). Schema migration v94 in `src/core/migrate.ts` adds a partial index `idx_facts_extract_conversation_session ON facts(source_id, source_session) WHERE source LIKE 'cli:extract-conversation-facts%'` (v14 precedent: `transaction:false` + invalid-index pre-drop on Postgres; plain CREATE INDEX on PGLite) so the doctor backlog query stays fast on million-fact brains. `src/commands/doctor.ts:computeConversationFactsBacklogCheck` is 3-state (SKIPPED when `cycle.conversation_facts_backfill.enabled=false` — no opt-out noise debt per Eng-v2 C9; OK when caught up; WARN when >10 pages lack the terminal audit row, with paste-ready remediation step composable via `gbrain doctor --remediate`). `src/commands/sources.ts:runAudit` extended with `facts_backfill_estimate: {pages, est_segments, est_cost_usd, types}` so `gbrain sources audit <id>` previews cost before any run. Schema-pack (v0.41.11.0): `gbrain-base.yaml` promotes `conversation` (temporal, extractable) + `atom` (annotation, NOT extractable — atoms ARE the extracted form) into the base seed; `concept.extractable` flips true semantically (cosmetic on backstop path because backstop uses hardcoded `ELIGIBLE_TYPES` in `src/core/facts/eligibility.ts:51`, not pack extractable — the original concept-grandfather migration was solving a phantom, dropped per Codex T3). `ALL_PAGE_TYPES` in `src/core/types.ts` extended with the two new types. Plan + all decisions persisted at `~/.claude/plans/system-instruction-you-are-working-linear-unicorn.md` and the CEO plan at `~/.gstack/projects/garrytan-gbrain/ceo-plans/2026-05-25-conversation-retrieval-upgrade.md`.
- `src/commands/extract.ts` — `gbrain extract links|timeline|all [--source fs|db] [--source-id <id>]`: batch link/timeline extraction. fs walks markdown files, db walks pages from the engine (mutation-immune snapshot iteration; use this for live brains with no local checkout). As of v0.12.1 there is no in-memory dedup pre-load — candidates are buffered 100 at a time and flushed via `addLinksBatch` / `addTimelineEntriesBatch`; `ON CONFLICT DO NOTHING` enforces uniqueness at the DB layer, and the `created` counter returns real rows inserted (truthful on re-runs). v0.22.1 (#417): `ExtractOpts.slugs?: string[]` enables incremental extract — when set, `extractForSlugs()` reads ONLY those slugs' files (single combined links+timeline pass) instead of the full directory walk. CLI `gbrain extract` keeps full-walk behavior; the cycle path threads sync's `pagesAffected` through. `walkMarkdownFiles(brainDir)` still runs at line 455 to build `allSlugs` for link resolution — see `TODOS.md` for replacing it with `engine.getAllSlugs()`. **v0.37.7.0 (#1204):** `--source-id <id>` flag scopes extraction to one brain source on federated brains. Resolved via `resolveSourceWithTier()` before any SQL runs; failures surface with a `gbrain sources list` hint. Closes the silent-collapse-to-`default` bug class for extract.
- `src/core/extract/receipt-writer.ts` + `src/core/extract/rollup-writer.ts` + `src/commands/extract-status.ts` + `src/commands/extract-explain.ts` + `src/commands/extract-benchmark.ts` + `src/core/schema-pack/scaffold-extractable.ts` (v0.41.23.0) — unified extract operator-surface wave. Every shipped extractor (deterministic `facts.conversation` in `src/commands/extract-conversation-facts.ts` + three LLM-backed cycle phases at `src/core/cycle/{extract-atoms,synthesize-concepts,propose-takes,extract-facts}.ts`) now writes ONE receipt page per run (`writeReceipt`) + UPSERTs a row to `extract_rollup_7d` (`upsertExtractRollup`). Receipt slug per D-EXTRACT-17: `extracts/{date}/{kind}/{source_id}/{run_id_short}/round-{N}.md`; frontmatter stamps BOTH `type: extract_receipt` AND `dream_generated: true` per D-EXTRACT-19 (belt+suspenders against extraction-loop guard drift). `extract_receipt` joins `ALL_PAGE_TYPES` in `src/core/types.ts`; `extracts/` prefix gets a 0.3x source-boost demote in `src/core/search/source-boost.ts` so receipts surface in search but never dominate user content. Migration v104 adds `extract_rollup_7d (kind, source_id, day, cost_usd, halt_count, eval_pass_count, eval_fail_count, round_completed_count, rollup_write_failures, updated_at)` with PK `(kind, source_id, day)` + `idx_extract_rollup_7d_day`. Rollup writes are best-effort with process-scoped error-dedup so transient DB failures bump `rollup_write_failures` instead of crashing the cycle. New `extract_health` doctor check reads the rollup for last 7 days, warns at halt-rate > 10% AND when rollup_write_failures > 0; pre-v104 brains report `ok` silently. Operator CLI surface: `gbrain extract status [--source-id ID] [--kind X] [--verbose] [--json]` (7-day rollup, sorted by halt_rate desc + cost desc, kubectl-style top-5 + "more rows" hint, stable `schema_version: 1` JSON envelope); `gbrain extract --explain <kind>` (resolution chain: pack-declared vs built-in cycle phase, prompt_template + fixture_corpus paths with `✓`/`(missing)` markers, last 7d rollup); `gbrain extract benchmark --pack X --kind Y` (loads pack fixture corpus through strict D-EXTRACT-21 path validation — rejects absolute paths, `..` traversal, null bytes, AND symlinks resolving outside pack root; v0.41.23 ships as a stub-reporter — LLM dispatch deferred to a follow-up release). Pack-author authoring loop: `src/core/schema-pack/manifest-v1.ts` widens `extractable` from `z.boolean()` to `z.union([z.boolean(), ExtractableSpecSchema])` (carries `prompt_template`, `fixture_corpus`, `eval_dimensions`, `benchmark_min_recall`, plus reserved `verifier_path` per D-EXTRACT-37 — parses but refuses at runtime in v0.41.23); new `extractableSpecsFromPack` + `getExtractableSpec` + `refuseVerifierPathInV042` helpers in `src/core/schema-pack/extractable.ts`; `gbrain schema scaffold-extractable <type> --pack <pack>` declares the type extractable in one verb, generates 5 placeholder fixtures + a prompt template stub under `packs/<pack>/{fixtures,prompts}/extract/`, refuses to overwrite without `--force`. Tests: 22 cases in `test/extractable-spec-widening.test.ts` (back-compat boolean shape + struct shape + D-EXTRACT-37 verifier_path refuse), 12 cases in `test/extract/receipt-writer.test.ts` (uses canonical PGLite block per CLAUDE.md R3+R4 — one engine per file with `resetPgliteState` in `beforeEach`), 17 cases in `test/extract/benchmark.test.ts` (path validation rejections + JSONL contract), 15 cases in `test/extract/status.test.ts` (pure aggregation + formatting), 15 cases in `test/schema-pack/scaffold-extractable.test.ts` (scaffold mechanics + explicit privacy-rule guards against real-name leakage), 8 cases in `test/doctor-extract-health.test.ts`. Plan persisted at `~/.claude/plans/system-instruction-you-are-working-stateless-dragonfly.md`. Deferred to a follow-up release: replay versioning + `gbrain extract replay --since v<sha>`; unified LLM dispatcher (deliberately respects v0.41.13 head comment that extraction is regex + cost-cap value-add lives at embed step).
- `src/commands/import.ts` — `gbrain import <path> [--source-id <id>]`: page import with the v0.34.2.0 path-set checkpoint described above. **v0.37.7.0 (#1167):** new `--source-id <id>` flag finally honored — pages route to the named source. Resolved via `resolveSourceWithTier()` at the boundary; the same flag is now consistent across `import`, `extract`, `graph-query`, and `sources current`. Pinned by `test/import-source-id.test.ts`.
- `src/commands/graph-query.ts` — `gbrain graph-query <slug> [--type T] [--depth N] [--direction in|out|both] [--include-foreign]`: typed-edge relationship traversal (renders indented tree). **v0.37.7.0 (#1153):** foreign-edge footer always present (`X foreign edges (use --include-foreign to traverse)`) so cross-source edges never disappear silently; `--include-foreign` widens the SQL filter to walk them. Pinned by `test/graph-query.test.ts`.
- `src/commands/sources.ts` — `gbrain sources {list,add,remove,archive,restore,archived,purge,current,status,audit}`. **v0.37.7.0 (#1222):** new `current [--json]` subcommand calls `resolveSourceWithTier()` and prints `source_id`, `tier` (one of `flag | env | dotfile | local_path | brain_default | seed_default`), and optional `detail`. The agent-facing decision table for which tier wins lives in `skills/conventions/brain-routing.md`. **v0.40.3.0 (productionized from PR #1314):** new `status [--json]` subcommand — read-only per-source dashboard (last sync, staleness, page count, embedding coverage, unacked failures). Thin wrapper around `buildSyncStatusReport` + `printSyncStatusReport` exported from `src/commands/sync.ts`. `--json` emits the stable `{schema_version: 1, sources, ...}` envelope on stdout for monitoring pipelines; bare invocation prints the human table to stdout (right-aligned numeric columns, kubectl-style). Filters input sources to `local_path IS NOT NULL AND archived IS NOT TRUE` so archived sources (which have their own `gbrain sources archived` surface) don't muddy the active-sync dashboard. Lives under `sources` (not `sync --status`) per D3 from the v0.40.3.0 plan-eng-review — reads and writes don't share a verb. **v0.40.9.0:** new `audit <id> [--json]` subcommand — read-only dry-run scan of a source repo's disk for size distribution + would-blocks + junk-pattern hits, WITHOUT touching the DB. Catches scraper junk and oversized content BEFORE sync. Walks `sources.local_path`, reads each markdown file, runs `assessContent()` from `src/core/content-sanity.ts`, aggregates by verdict (`ok | warn_oversize | hard_block_junk_pattern`). JSON envelope is stable for monitoring pipelines. Pinned by `test/sources-audit.test.ts` (not present in this wave; covered transitively by `test/content-sanity.test.ts` + `test/import-file-content-sanity.test.ts`). **v0.41.31.0 (P0a):** `gbrain sources status` (the live `runStatus` health table path, NOT just the `buildSyncStatusReport` dashboard) gains a `BACKFILL` column between `EMBED` and `FAILS`: `active(N)` beats `queued(N)` beats `idle`, sourced from `SourceMetrics.backfill_active` / `backfill_queued` in `src/core/source-health.ts`. Under federated_v2, `sync --all` defers embedding to per-source `embed-backfill` minion jobs, so an operator needs to SEE that deferred work after sync exits 0 instead of assuming it was lost. The data layer (`jobCountsBySource` in `source-health.ts`) widens its one `minion_jobs` SQL with two `COUNT(*) FILTER (WHERE name = 'embed-backfill' AND ...)` aggregates (active vs waiting/delayed/waiting-children) — best-effort, all-0 on pre-minions brains. Pinned by `test/source-health.test.ts`.
- `src/commands/reindex-frontmatter.ts` — `gbrain reindex-frontmatter`. **v0.37.7.0 (#1225):** wrapped the query path in the standard `withEngine(...)` lifecycle so `engine.connect()` runs before the first SQL call. Pre-fix the command `process.exit(1)`'d with a TypeError on first invocation. Pinned by `test/reindex-frontmatter-connect.test.ts`.
- `src/core/source-resolver.ts` — 6-tier source resolution. **v0.37.7.0:** new additive helper `resolveSourceWithTier(engine, explicit, cwd)` returns `{ source_id, tier: SourceTier, detail? }` alongside the existing `resolveSourceId()` (unchanged, no caller breakage). New exported const `SOURCE_TIER_NAMES = ['flag', 'env', 'dotfile', 'local_path', 'brain_default', 'seed_default']` so the JSON shape stays type-stable across releases. Order matches the 1-6 priority of `resolveSourceId()`. Consumed by `gbrain sources current`, `gbrain import --source-id`, `gbrain extract --source-id`, and the v0.37.7.0 `source_routing_health` doctor check. Pinned by `test/source-resolver-with-tier.test.ts` (uses `withEnv()` wrapper per the test-isolation lint). **v0.41.13.0 (#1434):** new tier 5.5 `sole_non_default` slots between `brain_default` and `seed_default`. When NO `sources.default` config is set AND exactly one registered source has `local_path` AND isn't `'default'`, auto-route to it. `SOURCE_TIER_NAMES` extended to 7 entries. New private `pickSoleNonDefaultSource(engine)` shared by both resolver entry points (cannot drift). Archived sources excluded (try/catch for pre-v34 brains). New exported `formatSoleNonDefaultNudge(sourceId): string | null` builds the user-facing stderr nudge (returns null when `GBRAIN_NO_SOLE_NON_DEFAULT_NUDGE=1`). `src/commands/sync.ts:1497-1519` rewired to call `resolveSourceWithTier` unconditionally so the new tier actually fires (codex caught the original plan shipping dead code). `src/commands/import.ts:96-128` mirrors the same wiring with the tier-gated nudge. Pinned by `test/source-resolver-sole-non-default.test.ts` (14 cases) + `test/sync-sole-non-default-routing.test.ts` (3 PGLite cases driving real `runSync` with stderr capture).
- `src/core/sync.ts` extension (v0.41.13.0, #1433) — `isSyncable` factored through a private `classifySync(path, opts): SyncableReason | null` helper. New exported `unsyncableReason(path, opts)` companion returns the same tagged reason or null when syncable. `SYNC_SKIP_FILES` lifted to a named export (the four canonical metafile basenames: `schema.md`, `index.md`, `log.md`, `README.md`). New `SyncableReason` union: `'metafile' | 'strategy' | 'pruned-dir' | 'include-glob-miss' | 'exclude-glob-hit'`. `src/commands/sync.ts:772` cleanup loop now guards on `unsyncableReason(path) === 'metafile'` so previously-indexed metafile pages (typically `log.md` from an older gbrain that didn't filter it) survive every re-sync. Honest scope: does NOT cover `manifest.deleted` (the upstream filter already strips metafiles, so `rm log.md` doesn't delete the page either — v0.42+ TODO for a `gbrain pages remove <slug>` operator surface). Pinned by `test/sync-isSyncable-shape.test.ts` (15 cases pinning the duality contract) + `test/sync-metafile-skip.serial.test.ts` (3 PGLite cases including the negative case — renamed `.md → .txt` still gets cleaned up properly).
- `src/core/import-file.ts` extension (v0.41.13.0, #1309) — identity-based dedup pre-check at `:427-490`. Calls the new `engine.findDuplicatePage?.(sourceId, {hash, frontmatterId})` (optional `?` so test doubles compile unchanged). Posture per codex review: SKIP when `frontmatter.id` matches (true external duplicate from overlapping ingest roots), WARN-ALWAYS on content_hash collision with different/missing `frontmatter.id` (templates and daily logs may legitimately share text), FAIL CLOSED on lookup error (silent fallthrough would mask the very bug this fixes), bypass via `--force-rechunk`. Soft-deleted pages excluded at the engine layer so tombstones don't block legitimate re-imports under new slugs. Pinned by `test/import-dedup-frontmatter-id.test.ts` (11 cases).
- `src/core/engine.ts` extension (v0.41.13.0) — two interface changes: (1) #1309 — new optional `findDuplicatePage?(sourceId, {hash, frontmatterId?}): Promise<{slug, id} | null>` method; identity precedence is content_hash OR frontmatter->>'id' both with `deleted_at IS NULL`; (2) #1436 — `resolveSlugs(partial, opts?)` signature extended with `{sourceId?, sourceIds?}` so the MCP fuzzy `get_page` path scopes by source (closes the source-bleed bug class that mirrored the v0.34.1 P0 seal for exact lookups). Field names match `sourceScopeOpts(ctx)` output so handlers can spread directly. Both signatures back-compatible — callers passing no opts get the pre-fix behavior. Plus a stable tiebreaker `ORDER BY score DESC, page_id ASC, chunk_id ASC` added to `searchVector` in both engines: when two chunks tie on score (basis-vector eval fixtures), older `page_id` wins. Closes the planner-non-determinism regression class — adding any new index to `pages` could previously flip ranking on tied scores between branches.
- `src/core/migrate.ts` v95 (v0.41.13.0, #1309) — `pages_dedup_partial_index` adds `CREATE INDEX pages_dedup_idx ON pages (source_id, content_hash) WHERE deleted_at IS NULL`. Postgres path uses `CREATE INDEX CONCURRENTLY` with `transaction: false` + pre-drops any invalid remnant from a prior failed attempt; PGLite uses plain `CREATE INDEX`. Powers `findDuplicatePage` hot path on 100K-page brains — query becomes O(log n) instead of O(n).
- `src/cli.ts` extension (v0.41.13.0, #1422) — `dream` dispatch at lines 1063-1080 binds the caught engine-connect error and emits `[dream] WARNING: could not connect to DB (...)` to stderr before falling through to filesystem-only phases. Pre-fix the catch swallowed silently and the user saw `gbrain dream` exit 0 with no clue why DB phases were skipped. The `runDream(null, ...)` no-DB fallback is preserved — filesystem phases still run honestly. Pinned by `test/cli-dream-engine-warn.test.ts` (2 subprocess cases against good + bad DATABASE_URL).
- `src/commands/autopilot.ts` extension (v0.37.7.0) — three changes for federated-brain co-existence and launchd hygiene. (1) **#1226 lockfile scope:** `LOCK_PATH` resolves via `gbrainPath('autopilot.lock')` so it honors `GBRAIN_HOME`. Two brains can run autopilot simultaneously without lock-stealing. Lock file now stores PID; startup checks `kill -0 <pid>` before refusing to start (codex CF11 PID-safety fix — stale lock from a crashed process no longer blocks a healthy autopilot). (2) **#1162 reconnect classifier:** new exported `classifyReconnectError(err)` returns `'recoverable' | 'unrecoverable'`. Unrecoverable causes the daemon to `process.exit(0)` and let launchd back off instead of the v0.37.6 loop that logged `config.database_url undefined` every 5s forever. (3) **launchd plist generator:** new exported pure function `generateLaunchdPlist(wrapperPath, home)` sets `ThrottleInterval=300` so launchd respects the exit-0 backoff. Both helpers pinned by `test/autopilot-lock-path.test.ts` + `test/autopilot-reconnect-classifier.test.ts`.
- `src/core/oauth-provider.ts` + `src/commands/serve-http.ts` extension (v0.37.7.0, #1166) — custom `/token` middleware that runs BEFORE the MCP SDK's `clientAuth`. The SDK does plaintext compare against the request's `client_secret`; gbrain stores SHA-256 hashes only, so every confidential-client `/token` request failed in v0.37.0–v0.37.6. The new middleware detects confidential auth via `Authorization: Basic` header OR `client_secret_post` form body (both shapes per RFC 6749 §2.3.1), verifies via `verifyClient(client_id, presented_secret)` (SHA-256 hash compare), and falls through to the SDK for public PKCE clients. Public clients (Claude Code, Cursor, every other PKCE-first MCP client) are unaffected — the SDK's clientAuth path still accepts them via the v0.34.1.0 NULL-`client_secret_hash` normalization. Pinned by `test/oauth-confidential-client.test.ts` (both `client_secret_basic` and `client_secret_post` paths).
- `src/core/sync.ts:pruneDir` extension (v0.37.7.0, #1169) — `pruneDir(name, parentDir?)` signature extended with optional `parentDir`. When provided, the helper additionally rejects directories containing `.git` as a FILE — the git submodule gitfile pattern (regular repos have `.git` as a DIRECTORY; submodules have it as a file pointing into the parent's `.git/modules/`). Sync + extract walkers thread `parentDir` through so the gitfile-as-FILE check fires per descend step. Best-effort: `statSync` failures (cross-platform permission edge) fall through and treat as a normal dir. Closes the phantom-import bug class where syncing a worktree-with-submodules silently walked into submodule trees. Pinned by `test/sync-walker-submodule.test.ts`.
- `src/core/minions/handlers/subagent.ts` extension (v0.37.7.0, #1151) — terminal-state short-circuit on resume. When a stored message thread already ends in `stop_reason: 'end_turn'`, the handler returns `{ ok: true }` immediately instead of issuing another `messages.create` call. Pre-fix, resume tried to re-prompt past `end_turn`, the Anthropic API rejected with a 400, and the worker classified the (already-successful) job as failed and dead-lettered it. Pinned by `test/subagent-handler.test.ts`.
- `src/commands/doctor.ts` extension (v0.37.7.0, T12+T13+T14) — three new checks wired into `runDoctor()` and the JSON envelope. (1) `checkSourceRoutingHealth(engine)` scans up to 200 pages on federated brains and flags pages whose `source_id` doesn't match what `resolveSourceWithTier()` would have picked for their `source_path`. Single-source brains short-circuit to `ok` ("no federation to check"). D5 200-page cap keeps doctor under 5s on huge brains; the cap is total across the brain, not per-source. (2) `checkOauthConfidentialHealth(engine)` probes registered confidential clients for `/token` reachability — warns when the v0.37.0–v0.37.6 plaintext-compare bug class would have rejected them. (3) `checkAutopilotLockScope()` is a pure-function check (no engine) that compares the resolved lock path to `$GBRAIN_HOME`; warns when `$GBRAIN_HOME` is set but the lock lives elsewhere, with a PID-safe inspection hint per codex CF11 (lock file holds the daemon PID; check `kill -0 <pid>` before considering deletion). All three are warn-only — they surface paste-ready fix hints without flipping the doctor exit code. Pinned by `test/doctor-v0_37_7_checks.test.ts`.
- `skills/conventions/brain-routing.md` (v0.37.7.0, #1222) — agent-facing convention skill documenting the canonical 6-tier source resolution chain (flag → env → dotfile → local_path → brain_default → seed_default) with paste-ready decision tables. Linked from CLAUDE.md's "Two organizational axes" section and from `gbrain sources current`'s hint output.
- `src/commands/doctor.ts` extension (v0.40.4.1) — `buildChecks(engine, args, dbSource): Promise<Check[]>` exported as a test seam. `runDoctor` is now a thin wrapper: `buildChecks → computeDoctorReport → render + process.exit`. All 10 `process.exit` sites stay in the wrapper; the two early-return paths (no engine, connection failure) return partial check lists instead of inline exits. No behavior change — observable output identical because the wrapper renders the same partial list. Pinned by `test/doctor-behavioral.test.ts` (13 cases: pure aggregation math over `computeDoctorReport`, orchestrator cases for `--fast` skip set + `--json` flag + no-engine partial path + snapshot of load-bearing check names) and `test/doctor-cli-smoke.serial.test.ts` (1 subprocess case spawning `bun run src/cli.ts doctor --json` against a fresh PGLite tempdir, asserting schema_version=2 envelope, status enum, non-empty checks array — the render-path coverage that buildChecks-only tests miss). Quarantined as `.serial.test.ts` because PGLite write-locks don't play with parallel runners.
- `src/core/cycle.ts` extension (v0.40.4.1) — `runPhaseLint` + `runPhaseBacklinks` gain the `export` keyword so behavioral tests can drive them directly. No body changes; documented as internal helpers exposed for test-only consumption (downstream code should NOT take a dependency). Pinned by `test/cycle-legacy-phases.test.ts` (11 cases across both phases: clean run → status='ok', partial fix → status='warn' with `dryRun` in details, dry-run path doesn't write, throw-from-lib → status='fail' with the wrapper's try/catch envelope populated). Future phase wrappers (sync, extract, embed, orphans, extract_facts, resolve_symbol_edges, recompute_emotional_weight) land as additional describes in the same file, not new files (TODOS NEW-2).
- `test/operations-trust-boundary.test.ts` + `scripts/check-operations-filter-bypass.sh` (v0.40.4.1) — operations trust-boundary contract coverage. Hybrid test design: pure assertions over all 74 ops (every op has a scope annotation; every mutating op has a non-read scope; `localOnly: true` ops are excluded from `operations.filter(op => !op.localOnly)`; the seven historically-sensitive localOnly ops snapshot-pinned by name) plus targeted handler-invocation regressions for the two historically-broken HTTP-callable classes: `submit_job` with `name='shell'` + `ctx.remote=true` MUST reject (the F7b HTTP MCP shell-job RCE class), and `search_by_image` with `image_path` + `ctx.remote=true` MUST reject (the D18 P0 image-leak class). `file_upload` and `sync_brain` deliberately omitted from handler-invocation tests because they're `localOnly: true` and that path would test an impossible production scenario (codex CMT-3). The shell guard greps `src/` for any module importing the `operations` value outside the canonical filter site at `src/commands/serve-http.ts` — three import shapes detected (destructured, aliased, namespace), explicit 10-entry allow-list with per-entry rationale, plus a literal-string check that `serve-http.ts` still contains `operations.filter(op => !op.localOnly)`. Wired into `bun run verify`.
- `src/core/content-sanity.ts` (v0.40.9.0, NEW) — pure assessor for the content-sanity defense wave. `assessContent(content, opts): SanityVerdict` returns one of three verdicts (`ok | warn_oversize | hard_block_junk_pattern | soft_block_oversize`) with `{reason, bytes, matched_pattern_name?}` detail. Six hand-vetted built-in junk patterns (Cloudflare challenge dumps, CAPTCHAs, 403 dumps, bare error-page titles) compiled at module load; operator literal substrings loaded via `loadOperatorLiterals()` from `src/core/content-sanity-literals.ts`. `ContentSanityBlockError` tagged class is the typed throw shape — every wrapper site (`gbrain import` CLI, `put_page` MCP op, `gbrain sync`, `/ingest` webhook) catches it via the existing exception flow rather than a parallel status check. The bytes-parity contract (D2) pins `Buffer.byteLength(content, 'utf8')` against the embedder's actual byte count so a 499K-byte page can't be soft-blocked on assessment then overflow on embed. Knob resolution chain: env > file (`~/.gbrain/config.json`) > DB > defaults — env wins for CI / one-off overrides, file is operator-set, DB plane is what `gbrain config set` writes. Four knobs: `content_sanity.bytes_warn` (default 50_000), `content_sanity.bytes_block` (default 500_000), `content_sanity.junk_patterns_enabled` (default true), `content_sanity.disabled` (default false; `GBRAIN_NO_SANITY=1` is the loud-stderr kill-switch with per-ingest warning). Pinned by `test/content-sanity.test.ts` (416 lines, 99 assertions across happy path, every junk pattern, bytes-parity, knob resolution, operator literal fail-soft).
- `src/core/content-sanity-literals.ts` (v0.40.9.0, NEW) — operator literal-substring loader. Reads `~/.gbrain/junk-substrings.txt`, one literal per non-comment non-blank line. Optional `# name=<id>` header pairs an identifier with the following literal so audit JSONL groups by site (`linkedin_auth_wall`, `reddit_blocked`, etc.). Fail-soft on ENOENT (missing file = empty array, no error). Loaded on every ingest. Deliberately literal substrings (NOT regex) to defeat ReDoS — the regex-flavored extension is filed for v0.41+ once a real ReDoS budget exists. Pinned by `test/content-sanity-literals.test.ts` (110 lines).
- `src/core/embed-skip.ts` (v0.40.9.0, NEW) — 5-site shared predicate for the soft-block embed-skip filter. Exports `shouldSkipEmbedding(frontmatter): boolean` (JS predicate consumed by callers that already hold the page in memory), `EMBED_SKIP_SQL_FRAGMENT` (the parameterized SQL clause shared by Postgres + PGLite engines via `executeRaw`), and `buildEmbedSkipMarker(reason: string)` (writes `frontmatter.embed_skip = {at: ISO_TIMESTAMP, reason}` so the JSONB shape stays uniform across the 5 read sites). The 5 sites are: `embed.ts --stale`, `embed.ts --all`, the `embed-stale` Minion helper, plus both engines' `listStaleChunks` + `countStaleChunks`. Single source of truth so the soft-block filter cannot drift across sites (the bug class Codex r1 caught). Pinned by `test/embed-skip.test.ts` (cross-site invariant + JSONB shape).
- `src/core/audit/content-sanity-audit.ts` (v0.40.9.0, NEW) — ISO-week JSONL audit at `~/.gbrain/audit/content-sanity-YYYY-Www.jsonl` built on the v0.40.4.0 `audit-writer.ts` primitive. Records every hard-block, soft-block, and warn-trip event with `{kind, source_id, slug, bytes, matched_pattern_name?, reason, ts}`. Doctor reads the last 7 days, aggregates by `(matched_pattern_name, source_id)`, surfaces "31 ingest blocks this week, 28 from straylight-brain" so operators see which scraper is the actual problem. Honors `GBRAIN_AUDIT_DIR` for shared-filesystem multi-host setups (documented caveat in the doctor message for ops that don't share the dir). Pinned by `test/audit/content-sanity-audit.test.ts` (219 lines, 219 assertions).
- `src/commands/doctor.ts` extension (v0.40.9.0) — three new checks wired into `runDoctor()` and the JSON envelope: `oversized_pages` (warns on pages exceeding `content_sanity.bytes_warn`), `scraper_junk_pages` (warns on pages that match any junk pattern despite being live in the DB — these escaped pre-v0.40.9.0 ingest), and `content_sanity_audit_recent` (reads the last 7 days of audit events, aggregates by pattern+source). Default scans the 1000 most-recent pages; new `--content-audit` flag opts into a full scan for the cleanup wave. All three are warn-only with paste-ready fix hints (junk page → `gbrain sources audit <id>` + `git rm` source-of-truth, oversize → split or accept).
- `src/commands/lint.ts` extension (v0.40.9.0) — two new lint rules: `huge-page` (flags pages exceeding `content_sanity.bytes_warn` threshold) and `scraper-junk` (flags pages matching any junk pattern). Both reuse `assessContent()` from `src/core/content-sanity.ts` so lint, doctor, and ingest share one assessor — adding a junk pattern automatically covers all three surfaces. `lint.ts` lifts DB config when `~/.gbrain/` is reachable (matches what `gbrain config set` writes); falls back to file/env on CI. Pinned by `test/lint-content-sanity.test.ts` (161 lines).
- `src/commands/embed.ts` extension (v0.40.9.0) — applies the `embed-skip` filter at all 5 stale-chunk sites: `runEmbedCore --stale`, `runEmbedCore --all`, the `embed-stale` Minion helper, plus both engines' `listStaleChunks` + `countStaleChunks` via `EMBED_SKIP_SQL_FRAGMENT`. A soft-blocked page is queryable by title and slug but its chunks never enter the embed sweep. The shared helper from `src/core/embed-skip.ts` is the regression guard — no per-site ad-hoc filter is allowed. Pinned by `test/embed-skip.test.ts`.
- `src/core/import-file.ts` extension (v0.40.9.0) — `importFromContent` is the narrow waist that every ingest path passes through (`gbrain import`, `gbrain sync`, `put_page` MCP, `/ingest` webhook). It now calls `assessContent()` BEFORE chunking; verdict `hard_block_junk_pattern` throws `ContentSanityBlockError` (which every wrapper site already catches via its exception flow); verdict `warn_oversize OR oversize-without-junk` sets `frontmatter.embed_skip` via `buildEmbedSkipMarker()` AND deletes any pre-existing chunks for the page in the same transaction so search can't surface stale chunks against content that's now soft-blocked. `gbrain import` honors `errors > 0` for non-zero exit (was silently exit-0 on failed files). `classifyErrorCode` in `src/core/sync.ts` recognizes the new `PAGE_JUNK_PATTERN` code so sync-failures.jsonl grouping bins these correctly. Pinned by `test/import-file-content-sanity.test.ts` (206 lines). — shared library for the v0.12.0 graph layer. extractEntityRefs (canonical, replaces backlinks.ts duplicate) matches both `[Name](people/slug)` markdown links and Obsidian `[[people/slug|Name]]` wikilinks as of v0.12.3. extractPageLinks, inferLinkType heuristics (attended/works_at/invested_in/founded/advises/source/mentions), parseTimelineEntries, isAutoLinkEnabled config helper. `DIR_PATTERN` covers `people`, `companies`, `deals`, `topics`, `concepts`, `projects`, `entities`, `tech`, `finance`, `personal`, `openclaw`. Used by extract.ts, operations.ts auto-link post-hook, and backlinks.ts.
- `src/core/zombie-reap.ts` (v0.28.1) — idempotent `installSigchldHandler()` so JS-spawned children get reaped via Bun's internal `waitpid()`. Bun (like Node) only auto-reaps when a SIGCHLD listener is registered; without it, every child the worker spawns (shell jobs, embed batches, sub-agents) becomes a zombie on exit and holds connection slots. Called once at module load from `src/cli.ts` (with Windows platform guard — SIGCHLD doesn't exist on Windows). Cross-file leak guard via `_uninstallSigchldHandlerForTests()` for tests. Layer 1 of the three-layer zombie defense; Layer 2 is tini-as-PID-1 wrapping the worker subtree (via `src/core/minions/spawn-helpers.ts`); Layer 3 is the container's own tini for hard Bun crashes.
- `src/core/minions/` — Minions job queue: BullMQ-inspired, Postgres-native (queue, worker, backoff, types, protected-names, quiet-hours, stagger, handlers/shell).
- `src/core/minions/queue.ts` — MinionQueue class (submit, claim, complete, fail, stall detection, parent-child, depth/child-cap, per-job timeouts, cascade-kill, attachments, idempotency keys, child_done inbox, removeOnComplete/Fail). `add()` takes a 4th `trusted` arg (separate from `opts` to prevent spread leakage); protected names in `PROTECTED_JOB_NAMES` require `{allowProtectedSubmit: true}` and the check runs trim-normalized (whitespace-bypass safe). v0.14.1 #219: `add()` plumbs `max_stalled` through with a `[1, 100]` clamp; omitted values let the schema DEFAULT (5) kick in. v0.19.0: `handleWallClockTimeouts(lockDurationMs)` is Layer 3 kill shot for jobs where `FOR UPDATE SKIP LOCKED` stall detection and the timeout sweep both fail to evict (wedged worker holding a row lock via a pending transaction). v0.19.1: `maxWaiting` coalesce path now uses `pg_advisory_xact_lock` keyed on `(name, queue)` to serialize concurrent submits for the same key, and filters on `queue` in addition to `name` so cross-queue same-name jobs don't suppress each other.
- `src/core/minions/worker.ts` — MinionWorker class (handler registry, lock renewal, graceful shutdown, timeout safety net). v0.14.0 abort-path fix: aborted jobs now call `failJob` with reason (`timeout`/`cancel`/`lock-lost`/`shutdown`) instead of returning silently. `shutdownAbort` (instance field) fires on process SIGTERM/SIGINT and propagates to `ctx.shutdownSignal` — shell handler listens to it; non-shell handlers don't. v0.22.1 (#403): per-job timeout fires `abort.abort(new Error('timeout'))` then a 30-second grace-then-evict safety net force-evicts the job from `inFlight` and marks it dead in DB if the handler ignores the abort signal — frees the slot even when a handler wedges (the 98-waiting-0-active prod incident driver). **v0.41.26.1 (supersedes #1567):** the lock-renewal cathedral wave. The `launchJob` setInterval block — which previously was `setInterval(async () => await renewLock(...))` — is the v0.41.22.1 production crash class (~39 worker exits/day from `unhandledRejection at renewLock` during PgBouncer connection rotation). Replaced with a thin sync wrapper around the new pure `runLockRenewalTick` function from `src/core/minions/lock-renewal-tick.ts`. Five additional gaps closed in the same wave: (1) `cancelled` flag captured in the timer closure stops in-flight IIFEs from writing misleading audit events after the job ended; (2) re-entrancy guard (`tickInFlight`) plus per-call `Promise.race` timeout (`GBRAIN_LOCK_RENEWAL_CALL_TIMEOUT_MS`, default `lockDuration/3`) so a hung renewLock can't wedge the worker indefinitely; (3) time-based abort (`Date.now() - lastSuccessfulRenewalAt >= lockDuration - GBRAIN_LOCK_RENEWAL_SAFETY_MARGIN_MS`) replaces count-based, so we release the lock BEFORE another worker can reclaim; (4) explicit `.catch()` on the stored `executeJob(...).finally(...)` promise closes the SECOND unhandledRejection vector (if failJob throws during the same DB outage); (5) `INFRASTRUCTURE_ABORT_REASONS = new Set(['lock-renewal-failed', 'lock-lost'])` is exported; executeJob's catch skips `failJob` for these reasons so PgBouncer blips no longer dead-letter healthy jobs (the stall detector reclaims cleanly with the lock already expired). The 30s grace-evict safety net moved out of the `job.timeout_ms`-only branch into a generic abort listener that fires for ANY abort reason. CI guard `scripts/check-worker-lock-renewal-shape.sh` (wired into `bun run verify`) asserts the bug pattern `lockTimer = setInterval(async ...)` stays absent AND `launchJob` continues to call `runLockRenewalTick` so the test seam survives refactors. Behavior pinned by `test/worker-lock-renewal.test.ts` (18 hermetic state-machine cases over the pure function), `test/audit/lock-renewal-audit.test.ts` (11 cases), `test/scripts/check-worker-lock-renewal-shape.test.ts` (5 fixture-driven meta-tests). **v0.28.1 engine-ownership invariant:** `start()` no longer calls `engine.disconnect()` on shutdown — that was a leaky abstraction (the worker disconnected an engine it didn't own). The CLI handler in `src/commands/jobs.ts case 'work'` now owns engine lifecycle via try/finally with loud error logging on disconnect failure. Pinned by `test/worker-shutdown-disconnect.test.ts` asserting the inverse (`disconnectSpy).not.toHaveBeenCalled()`). **v0.34.3.0:** RSS watchdog metric switched to non-file-backed pages on Linux. New exports `parseRssFromProcStatus(status)` (pure parser, exported for unit tests) and `getAccurateRss(readStatus?)` (reads `/proc/self/status` for `RssAnon + RssShmem`, falls back to `process.memoryUsage().rss` on macOS / restricted containers / kernel <4.5). The default `getRss` injected into `WorkerOpts` is now `getAccurateRss` instead of `process.memoryUsage().rss`. Closes the prod incident where VmRSS inflated to 7GB on a 96K-page brain (file-backed git packfile mmaps) while heap stayed at ~100MB; the watchdog was firing every autopilot cycle. M1 parser fix uses field-presence regex checks so `RssAnon: 0 + RssShmem: 512` (shmem-only worker case) parses correctly instead of falling through to VmRSS. Pinned by `test/worker-rss.test.ts` (11 cases).
- `src/core/minions/supervisor.ts` — MinionSupervisor process manager. Spawns `gbrain jobs work` as a child, restarts on crash with exponential backoff, periodic health check. v0.22.1 (#406): `consecutiveHealthFailures` counter; on 3 consecutive failures emits `health_warn` with `reason: 'db_connection_degraded'` and calls `engine.reconnect()` to swap in a fresh pool, then resets the counter. Worker exit classifier emits `likely_cause` field on `worker_exited` events: `oom_or_external_kill` (SIGKILL), `graceful_shutdown` (SIGTERM), `runtime_error` (code 1), `clean_exit` (code 0), `unknown`. **v0.28.1:** consumes `detectTini()` + `buildSpawnInvocation()` from `src/core/minions/spawn-helpers.ts` to wrap the worker subtree in tini-as-PID-1 when tini is on `PATH` (handles native-addon zombie reaping that the in-process SIGCHLD reaper can't reach). Exposes `isTiniDetected` read-only accessor for tests. **v0.34.3.0:** spawn-and-respawn loop extracted into the shared `ChildWorkerSupervisor` core (see entry below). MinionSupervisor now composes the inner class via `runSuperviseLoop()` → `new ChildWorkerSupervisor({...})` and maps `ChildSupervisorEvent` shapes back through the existing `emit()` SupervisorEvent channel — JSONL audit consumers see byte-compatible output across the rename. PID lock, signal handlers, health check, and `process.exit` on max-crashes stay in MinionSupervisor (standalone-daemon concerns). The pre-shipped reset-to-0-on-code=0 hunk that originally fixed the prod crash-counter incident is gone; the same fix lives in the shared core under the D1 amendment (code=0 leaves `crashCount` untouched, so a worker alternating real crashes + watchdog drains still trips `max_crashes`). D2 `cleanRestartBudget` (default 10 restarts per 60s) caps the macOS/non-Linux-fallback tight-loop by emitting `health_warn { reason: 'clean_restart_budget_exceeded' }` plus backoff after the threshold trips. `shutdown()` drains via `childSupervisor.killChild('SIGTERM')` + `awaitChildExit(35_000)` instead of reaching into `this.child` directly. Pinned by `test/supervisor.test.ts` (16 cases; existing tests that previously relied on clean-exit-as-crash semantics now use exit-1 workers since clean exits no longer count) and `test/supervisor-tini.test.ts`.
- `src/core/minions/child-worker-supervisor.ts` (v0.34.3.0) — shared spawn-and-respawn core extracted from `MinionSupervisor` so it can be reused by both `MinionSupervisor` (standalone `gbrain jobs supervisor` daemon) and `src/commands/autopilot.ts` (autopilot daemon). Pre-v0.34.3.0 the two consumers maintained parallel spawn loops that drifted into the same bug class — Codex caught it during plan-eng-review on PR #1003. Pure class: NO PID file, NO signal handlers, NO `process.exit`, NO health check. Lifecycle events fire via injected `onEvent: (ChildSupervisorEvent) => void` callback so each composer routes to its own log/audit channel. **D1 exit classifier:** `code === 0` leaves `crashCount` UNCHANGED (preserves flap detection across mixed exit sequences — a worker that alternates `exit 1 / exit 0 / exit 1 / exit 0` correctly trips `max_crashes` after 10 real crashes regardless of intervening clean exits). `code != 0` follows the existing `runDuration > stableRunResetMs ? 1 : ++crashCount` rule. **D2 clean-restart budget:** sliding window tracks code=0 exits; when count exceeds `cleanRestartBudget` (default 10) inside `cleanRestartWindowMs` (default 60s), emits `health_warn { reason: 'clean_restart_budget_exceeded' }` and applies `cleanRestartBudgetBackoffMs` (default 1s) before the next spawn. Caps the worst-case tight-loop on macOS / restricted containers / kernel <4.5 where the worker's RSS watchdog falls back to VmRSS. Public read-only accessors `childAlive`, `inBackoff`, `crashCount` for composer health checks; `killChild(signal)` + `awaitChildExit(timeoutMs)` for shutdown paths. `awaitChildExit` short-circuits when `child.exitCode !== null || child.signalCode !== null` (regression caught in pre-landing /review: pre-fix, fast-SIGTERM responders caused a 35-second shutdown hang because the late `once('exit', ...)` listener never fired). Test hooks: `_backoffFloorMs` skips the real backoff curve, `_now` injects a fake clock. Pinned by `test/child-worker-supervisor.test.ts` (7 cases: D1 classifier with code=0 not counted, interleaved exits still trip max_crashes, stable-run + clean-exit interaction across faked 6-minute run, D2 budget triggers backoff + health_warn, budget config is per-instance, awaitChildExit short-circuit, event-shape regression). Plan that produced the design lives at `~/.claude/plans/this-is-a-real-sleepy-sketch.md`.
- `src/core/minions/spawn-helpers.ts` (v0.28.1) — pure `detectTini()` + `buildSpawnInvocation()` helpers consumed by both `supervisor.ts` and `autopilot.ts`. Resolves the DRY violation between the two spawn sites and makes the tini wrapping testable without `mock.module()` (rule R2 of `scripts/check-test-isolation.sh`). `detectTini()` calls `execFileSync('which', ['tini'])` with explicit `env: process.env` so Bun sees runtime PATH mutations (the env-snapshot bug fix). `buildSpawnInvocation(tiniPath, cmd, args)` returns `{cmd, args}` with tini prepended when present, or the bare invocation otherwise. Pinned by `test/spawn-helpers.test.ts` (5 cases) and `test/supervisor-tini.test.ts` (4 cases).
- `src/core/minions/types.ts` — `MinionJobInput` + `MinionJobStatus` + handler context types. `MinionJobInput.max_stalled` (new in v0.14.1) is optional; omitted values let the schema DEFAULT (5) kick in, provided values are clamped to `[1, 100]`.
- `src/core/minions/protected-names.ts` — side-effect-free constant module exporting `PROTECTED_JOB_NAMES` + `isProtectedJobName()`. Kept pure so queue core can import without loading handler modules.
- `src/core/minions/handlers/shell.ts` — `shell` job handler. Spawns `/bin/sh -c cmd` (absolute path, PATH-override-safe) or `argv[0] argv[1..]` (no shell). Env allowlist: `PATH, HOME, USER, LANG, TZ, NODE_ENV` + caller `env:` overrides + (v0.36.5.0) `inherit:`-resolved keys. UTF-8-safe stdout/stderr tail via `string_decoder.StringDecoder`. Abort (either `ctx.signal` or `ctx.shutdownSignal`) fires SIGTERM → 5s grace → SIGKILL on child. Requires `GBRAIN_ALLOW_SHELL_JOBS=1` on worker (gated by `registerBuiltinHandlers`). **v0.36.5.0:** `ShellJobParams.inherit?: string[]` is a free-form list of snake_case config-key names. The worker resolves each via `loadConfig()` and injects the value under the derived env key (`database_url` → `GBRAIN_DATABASE_URL`; everything else uppercased). Names persist in `minion_jobs.data` (and the shell-audit JSONL); values never do. The canonical validator `validateShellJobParams` (sibling file `shell-validate.ts`) runs **pre-enqueue** in both submit surfaces — `gbrain jobs submit shell` (jobs.ts:271) AND `submit_job` op for `name='shell'` (operations.ts:2085). The handler-entry re-validation here is defense-in-depth. Closes the codex F-CDX-1 load-bearing bug class where validation in the handler ran AFTER `queue.add()` persisted the row. The validator does NOT police which config keys the agent inherits — same-uid trust model treats the agent as a peer of the worker.
- `src/core/minions/handlers/shell-inherit.ts` (v0.36.5.0, NEW) — three small helpers, no closed enum. `INHERIT_NAME_RE` (`/^[a-z][a-z0-9_]*$/`) is the snake_case shape guard used by the validator; rejects `__proto__`, leading-underscore, uppercase, and path-traversal shapes so audit logs stay readable and prototype-pollution lookups can't smuggle through. `deriveEnvKey(name)` maps config-key → child-env-key (`name.toUpperCase()` with one override: `database_url` → `GBRAIN_DATABASE_URL` because plain `DATABASE_URL` is ambiguous). `resolveInheritValue(cfg, name)` is the value lookup; uses `Object.hasOwn` to defeat prototype-pollution lookups, returns undefined for missing / non-string / empty-string values. An earlier closed-enum design (hardcoded `INHERITABLE` record with shadow-keys per name) was abandoned because the agent and worker share a uid — refusing to let the agent inherit arbitrary config keys defends nothing in that trust model.
- `src/core/minions/handlers/shell-validate.ts` (v0.36.5.0, NEW) — `validateShellJobParams(data, opts?)` shared pre-enqueue validator. Throws `UnrecoverableError` with paste-ready operator hints on every failure path. Three rules: (1) existing cmd/argv/cwd/env shape, (2) inherit array shape + snake_case regex per element (prototype-pollution defense), (3) fail-fast on missing config value with `gbrain config set <key>` hint. Also accepts optional `redact_secrets?: boolean` for output-side scrubbing. The validator deliberately does NOT police WHICH secrets the agent passes — single-uid trust model. Test seam: `opts.config` lets unit tests drive the validator hermetically without mocking the module. The defense-in-depth re-call at `shell.ts` handler entry catches pre-existing rows submitted before v0.36.5.0.
- `src/core/minions/handlers/shell-redact.ts` (v0.36.5.0, NEW) — opt-in output-side scrubbing for shell-job stdout/stderr. Pure `redactSecretsInText(text, secrets)` function: string-mode `replaceAll` so regex metacharacters in values stay literal. When the caller passes `redact_secrets: true` (or `--redact-secrets` on the CLI), the handler builds a Map of inherit-name → resolved-value and post-processes both tails before throw/return, so the persisted `result.stdout_tail` / `result.stderr_tail` / `error_text` carry `<REDACTED:name>` instead of the value. Only `inherit:`-resolved values are scrubbed; caller-supplied `env:` values stay through (those are the agent's "fine in the row" channel). Heuristic — defeats the common-case `echo "$GBRAIN_DATABASE_URL"` echo, not adversarial encode-then-print. Default `false` for back-compat.
- `src/core/config.ts:ensureGitignore` (v0.36.5.0) — idempotent retroactive writer of `~/.gbrain/.gitignore` (single line `*`). Called from `saveConfig()` so every config-writing path lays it down, AND from `runPostUpgrade()` so existing users pick it up on next `gbrain upgrade`. Never clobbers a user-customized `.gitignore` (checks file exists + content non-empty before writing). Honest scope, named in CHANGELOG: blocks casual `git add ~/.gbrain` from inside an enclosing worktree, but does NOT cover already-tracked files, screenshots, backups (Time Machine / iCloud / Dropbox), or `git add -f`. The doctor check `home_dir_in_worktree` surfaces what `.gitignore` can't.
- `src/commands/doctor.ts:home_dir_in_worktree` (v0.36.5.0) — filesystem check walking up from `gbrainPath()` toward `$HOME` looking for either a `.git` directory (main repo) or `.git` file (linked worktree pointer; Conductor + git-worktrees topology). Walk terminates at `$HOME` so a `.git` above the user's home doesn't false-positive. Honors `GBRAIN_HOME` (gbrain appends `.gbrain` to the override). Warn (not fail) with worktree-root path + paste-ready fix pointing at `GBRAIN_HOME` override or moving the brain.
- `src/core/minions/handlers/shell-audit.ts` — per-submission JSONL audit trail at `~/.gbrain/audit/shell-jobs-YYYY-Www.jsonl` (ISO-week rotation; override via `GBRAIN_AUDIT_DIR`). Best-effort: `mkdirSync(recursive)` + `appendFileSync`; failures logged to stderr, submission not blocked. Logs cmd (first 80 chars) or argv (JSON array). Never logs env values.
- `src/core/minions/handlers/supervisor-audit.ts` — supervisor lifecycle JSONL audit at `~/.gbrain/audit/supervisor-YYYY-Www.jsonl` (ISO-week rotation; shares `computeIsoWeekName()` helper with `shell-audit.ts`). `writeSupervisorEvent(emission, supervisorPid)` appends one line per supervisor event (`started`, `worker_spawned`, `worker_exited`, `backoff`, `health_warn`, `health_error`, `max_crashes_exceeded`, `shutting_down`, `stopped`, `worker_spawn_failed`). `readSupervisorEvents({sinceMs})` is the readback path for `gbrain doctor`. **v0.35.5.0:** new exports `isCrashExit(event)`, `summarizeCrashes(events)`, `CrashSummary` type, and `CLEAN_EXIT_CAUSES` denylist (`'clean_exit' | 'graceful_shutdown'`). Single regression point — both `gbrain doctor` (Lane D supervisor check at `doctor.ts:1011-1043`) and `gbrain jobs supervisor status` (`jobs.ts:803-826`) import from here so the two CLI surfaces cannot drift. `isCrashExit` classifies a single `worker_exited` event against the denylist: `clean_exit` / `graceful_shutdown` are NON-crashes; everything else (`runtime_error`, `oom_or_external_kill`, `unknown`, AND any future `likely_cause` value added upstream in `child-worker-supervisor.ts`) is a crash. Pre-v0.34 audit lines lacking `likely_cause` fall back to `code !== 0`. `summarizeCrashes` returns `{total, by_cause: {runtime_error, oom_or_external_kill, unknown, legacy}, clean_exits}` so dashboards bind to named buckets — the `legacy` bucket catches BOTH pre-v0.34 fallback entries AND future unrecognized `likely_cause` values, fail-loud instead of silent underreport. Denylist-over-allowlist was a codex outside-voice catch during `/plan-eng-review` — the bug being fixed (read sites counting every `worker_exited` as a crash, inflating to 120+/day on healthy brains after v0.34.3.0 watchdog drains) was itself an allowlist-of-event-names. Pinned by `test/supervisor-audit.test.ts` (14 cases: 9-case `isCrashExit` branch matrix including denylist regression guard for unrecognized future causes + non-exit-event defensive case, 5-case `summarizeCrashes` aggregator including unrecognized-cause routing to legacy + null-code edge case) and 4 source-grep wiring assertions in `test/doctor.test.ts` guarding both surfaces against drift.
- `src/core/minions/backpressure-audit.ts` (v0.19.1) — sibling of shell-audit.ts for `maxWaiting` coalesce events. JSONL at `~/.gbrain/audit/backpressure-YYYY-Www.jsonl`. Fires one line per coalesce with `(queue, name, waiting_count, max_waiting, returned_job_id, ts)`. Closes the silent-drop vector the v0.19.0 maxWaiting guard introduced.
- `src/core/minions/handlers/subagent.ts` (v0.15) — LLM-loop handler. Two-phase tool persistence (pending → complete/failed), replay reconciliation for mid-dispatch crashes, dual-signal abort (`ctx.signal` + `ctx.shutdownSignal`), Anthropic prompt caching on system + tool defs. `makeSubagentHandler({engine, client?, ...})` factory; `MessagesClient` is an injectable interface the real SDK implements structurally. Throws `RateLeaseUnavailableError` (renewable) when rate-lease capacity is full. **v0.30.2:** Anthropic 400 `prompt is too long` responses (status 400 + body matches `/prompt is too long|prompt_too_long|context.*length/i`) classify as `UnrecoverableError` so the job goes straight to `dead` on first attempt instead of stalling three times before dead-lettering. Catches both initial-prompt overflow and turn-N tool-loop accumulation that the chunker in `synthesize.ts` can't bound ahead of time.
- `src/core/minions/handlers/subagent-aggregator.ts` (v0.15) — `subagent_aggregator` handler. Claims AFTER all children resolve (queue changes guarantee every terminal child posts a `child_done` inbox message with outcome). Reads inbox via `ctx.readInbox()`, builds deterministic mixed-outcome markdown summary. No LLM call in v0.15.
- `src/core/minions/handlers/subagent-audit.ts` (v0.15) — JSONL audit + heartbeat writer at `~/.gbrain/audit/subagent-jobs-YYYY-Www.jsonl`. Events: `submission` (one line per submit) + `heartbeat` (per turn boundary: `llm_call_started | llm_call_completed | tool_called | tool_result | tool_failed`). Never logs prompts or tool inputs. `readSubagentAuditForJob(jobId, {sinceIso})` is the readback path for `gbrain agent logs`.
- `src/core/minions/rate-leases.ts` (v0.15) — lease-based concurrency cap for outbound providers (default key `anthropic:messages`, max via `GBRAIN_ANTHROPIC_MAX_INFLIGHT`). Owner-tagged rows with `expires_at` auto-prune on acquire; `pg_advisory_xact_lock` guards check-then-insert; CASCADE on owning job deletion. `renewLeaseWithBackoff` retries 3x (250/500/1000ms).
- `src/core/minions/wait-for-completion.ts` (v0.15) — poll-until-terminal helper for CLI callers. `TimeoutError` does NOT cancel the job; `AbortSignal` exits without throwing. Default `pollMs`: 1000 on Postgres, 250 on PGLite inline.
- `src/core/minions/transcript.ts` (v0.15) — renders `subagent_messages` + `subagent_tool_executions` to markdown. Tool rows splice under their owning assistant `tool_use` by `tool_use_id`. UTF-8-safe truncation; unknown block types fall through to fenced JSON.
- `src/core/minions/plugin-loader.ts` (v0.15) — `GBRAIN_PLUGIN_PATH` discovery. Absolute paths only, left-wins collision, `gbrain.plugin.json` with `plugin_version: "gbrain-plugin-v1"`, plugins ship DEFS only (no new tools), `allowed_tools:` validated at load time against the derived registry.
- `src/core/minions/tools/brain-allowlist.ts` (v0.15, extended v0.23, v0.29, v0.35.3.0) — derives subagent tool registry from `src/core/operations.ts`. 13-name allow-list as of v0.29 (was 11). By default `put_page` schema is namespace-wrapped per subagent (`^wiki/agents/<subagentId>/.+`). **v0.23 trusted-workspace path:** when `BuildBrainToolsOpts.allowedSlugPrefixes` is set, the put_page schema instead describes the prefix list to the model and the OperationContext is threaded with `allowedSlugPrefixes`. Trust comes from `PROTECTED_JOB_NAMES` gating subagent submission — MCP cannot reach this field. Only cycle.ts (synthesize/patterns) and direct CLI submitters set it. **v0.29:** `get_recent_salience` + `find_anomalies` added to the allow-list. `get_recent_transcripts` deliberately NOT added — all subagent calls run with `ctx.remote === true`, and the v0.29 trust gate rejects remote callers, so adding it would always reject (footgun). The cycle synthesize phase already calls `discoverTranscripts` directly. **v0.35.3.0:** `paramsToInputSchema()` now consumes `paramDefToSchema` from `src/mcp/tool-defs.ts` instead of its own inline destructure. Required-aggregation at the tool-def level stays here (out of scope for the shared helper, which is per-param). Closes the third drift site in the ParamDef→JSON Schema bug class.
- `src/mcp/tool-defs.ts` (v0.15, v0.35.3.0) — extracted `buildToolDefs(ops)` helper. MCP server + subagent tool registry both call it; byte-for-byte equivalence pinned by `test/mcp-tool-defs.test.ts`. **v0.35.3.0:** exports the new recursive `paramDefToSchema(p: ParamDef)` helper — single source of truth for ParamDef→JSON Schema mapping. Three consumers now share one mapper: `buildToolDefs` (stdio MCP), `src/commands/serve-http.ts:837` (HTTP MCP `tools/list`), and `src/core/minions/tools/brain-allowlist.ts:84` (subagent tool registry). Pre-v0.35.3, three inline destructures had drifted across the surface — the live HTTP MCP path dropped `items` on every array param after a v0.32 review caught only the stdio side. Recursive on `items` so nested array-of-arrays preserves inner shape on the wire. Key ordering (type, description, enum, default, items) is intentional — matches the pre-v0.35.3 inline mappers so JSON.stringify output stays byte-stable. `test/mcp-tool-defs.test.ts` adds a `findArrayWithoutItems` walker that fails the suite with a property path on any future `type: 'array'` lacking `items.type`.
- `src/core/minions/attachments.ts` — Attachment validation (path traversal, null byte, oversize, base64, duplicate detection)
- `src/commands/agent.ts` (v0.16) — `gbrain agent run <prompt> [flags]` CLI. Submits `subagent` (or N children + 1 aggregator) under `{allowProtectedSubmit: true}`. Single-entry `--fanout-manifest` short-circuits. Children get `on_child_fail: 'continue'` + `max_stalled: 3`. `--follow` is the default on TTY; streams logs + polls `waitForCompletion` in parallel. Ctrl-C detaches, does not cancel.
- `src/commands/agent-logs.ts` (v0.16) — `gbrain agent logs <job> [--follow] [--since]`. Merges JSONL heartbeat audit + `subagent_messages` into a chronological timeline. `parseSince` accepts ISO-8601 or relative (`5m`, `1h`, `2d`). Transcript tail renders only for terminal jobs.
- `src/commands/jobs.ts` — `gbrain jobs` CLI subcommands + `gbrain jobs work` daemon. **v0.28.1:** `case 'work'` now wraps `worker.start()` in try/finally and owns engine lifecycle — calls `engine.disconnect()` on shutdown with loud error logging on failure. Replaces the prior call inside `MinionWorker.start()` (which violated engine ownership: the worker disconnected an engine it didn't own, and clobbered the module-level singleton on PostgresEngine via the now-fixed idempotency bug). Pool slots now free immediately on shutdown instead of waiting for TCP keepalive (~minutes). v0.13.1 surfaces the full `MinionJobInput` retry/backoff/timeout/idempotency surface as first-class CLI flags on `jobs submit`: `--max-stalled`, `--backoff-type fixed|exponential`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key`. `jobs smoke --sigkill-rescue` is the opt-in regression guard for #219. v0.16 wires `registerBuiltinHandlers` to always register `subagent` + `subagent_aggregator` (no env flag — `ANTHROPIC_API_KEY` is the natural cost gate, trust is via `PROTECTED_JOB_NAMES`) and loads `GBRAIN_PLUGIN_PATH` plugins at worker startup with a loud startup-line per plugin. `shell` handler still gated by `GBRAIN_ALLOW_SHELL_JOBS=1` (RCE surface, separate concern). v0.22.10 (#521): the `autopilot-cycle` handler now forwards `job.data.phases` to `runCycle` (was previously discarded — caller-supplied phase selection silently became a full cycle). Phases are validated against `ALL_PHASES` from `src/core/cycle.ts`; invalid names are filtered out and an empty/missing array falls back to the default 6-phase cycle. v0.22.13 (PR #490 CODEX-1+CODEX-4): `sync` handler now resolves `sourceId` at entry by looking up `sources.local_path` (mirrors `cycle.ts:480`'s autopilot fix from PR #475) so multi-source brains read the per-source `last_commit` anchor instead of the global config key. Concurrency routed through the shared `autoConcurrency()` policy in `src/core/sync-concurrency.ts` instead of the prior hardcoded `4`; PGLite stays serial. `noEmbed` default is `true` (embed is a separate job — submit `gbrain embed --stale` after sync, or rely on the autopilot cycle's embed phase). **v0.35.5.0:** `gbrain jobs supervisor status` at `jobs.ts:803-826` now consumes `summarizeCrashes()` from `src/core/minions/handlers/supervisor-audit.ts` for cross-surface parity with `gbrain doctor`. JSON output adds `crashes_by_cause: {runtime_error, oom_or_external_kill, unknown, legacy}` + `clean_exits_24h` fields so dashboards bind to named buckets; human output gains a per-cause line under `Crashes (24h)` plus a `Clean exits (24h)` line. Pre-fix the read site at `jobs.ts:805` counted every `worker_exited` event as a crash regardless of `likely_cause` — the same bug class the v0.35.5.0 doctor fix closes. Pinned by the 4 source-grep wiring assertions in `test/doctor.test.ts` that require the per-cause breakdown substrings (`crashes_by_cause`, `clean_exits_24h=`) to appear in BOTH `doctor.ts` and `jobs.ts`.
- `src/commands/features.ts` — `gbrain features --json --auto-fix`: usage scan + feature adoption salesman
- `src/commands/autopilot.ts` — `gbrain autopilot --install`: self-maintaining brain daemon (sync+extract+embed). **v0.28.1:** consumes `detectTini()` from `src/core/minions/spawn-helpers.ts` and resolves it once at startup instead of per worker respawn (was paying an `execFileSync` cost on every restart). **v0.34.3.0:** inline spawn-and-respawn loop replaced with a `ChildWorkerSupervisor` instance. Drops `crashCount`, `lastWorkerStartTime`, `STABLE_RUN_RESET_MS`, `startWorker`, and the inline `child.on('exit')` block — all consolidated into the shared core. `--max-rss 2048` and `maxCrashes: 5` preserved from the legacy loop. `onMaxCrashesExceeded` now routes through autopilot's own `shutdown('max_crashes')` so the autopilot lockfile gets cleaned up (pre-refactor the inline loop called `process.exit(1)` directly and bypassed cleanup). `shutdown()` drains via `childSupervisor.killChild('SIGTERM')` + `awaitChildExit(35_000)` instead of `workerProc.kill()`. Pinned by `test/autopilot-supervisor-wiring.test.ts` (6 static-shape regression guards: composes ChildWorkerSupervisor not the legacy inline names, `--max-rss 2048` in argv, `maxCrashes: 5` literal, shutdown-via-callback wiring, no workerProc reference). Closes the parallel-supervisor bug class Codex flagged during plan-eng-review.
- `src/mcp/server.ts` — MCP stdio server (generated from operations). v0.22.7: tool-call handler delegates to `dispatchToolCall` from `src/mcp/dispatch.ts` so stdio + HTTP transports share one validation, context-build, and error-format path. **v0.34.1.0 (#870):** stdin `'end'` / `'close'` shutdown hooks are skipped when `process.env.MCP_STDIO === '1'`. Gateway-piped stdio MCP wrappers (OpenClaw's `bundle-mcp`, similar) pipe the JSON-RPC handshake then close their stdin half; pre-fix this killed the server before the first tool call landed. Signal handlers (SIGTERM / SIGINT / SIGHUP) and the parent-process watchdog still cover legitimate disconnects. `src/commands/serve.ts` exposes `ServeOptions.mcpStdio?: boolean` as a test seam so the runtime guard is exercisable without process.env mutation. Pinned by `test/serve-stdio-lifecycle.test.ts`.
- `src/mcp/dispatch.ts` (v0.22.7) — Shared tool-call dispatch consumed by both stdio (`server.ts`) and HTTP transports. Exports `dispatchToolCall(engine, name, params, opts)`, `buildOperationContext(engine, params, opts)`, and `validateParams(op, params)`. Single source of truth for `(ctx, params)` handler arg order and the 5-field `OperationContext` shape (engine + config + logger + dryRun + remote). Defaults to `remote: true` (untrusted); local CLI callers pass `remote: false`. Closed F1/F2/F3 drift bugs in the original v0.22.5 HTTP transport. **v0.26.9 (F8):** adds `summarizeMcpParams(opName, params)` — privacy-preserving redactor for `mcp_request_log` and the admin SSE feed. Returns `{redacted, kind, declared_keys, unknown_key_count, approx_bytes}`. Intersects submitted top-level keys against the operation's declared `params` allow-list (declared keys preserved as a sorted array for debug visibility; unknown keys counted but never named, closing the attacker-controlled-key-name leak). Byte counts bucketed up to nearest 1KB so an attacker can't binary-search secret-content sizes via repeated probes. Operators on a personal laptop who want raw payload visibility opt back in with `gbrain serve --http --log-full-params` (loud stderr warning at startup). Canonical helper — new logging code paths route through it rather than `JSON.stringify(params)`.
- `src/mcp/rate-limit.ts` (v0.22.7) — Bounded-LRU token-bucket limiter. `buildDefaultLimiters()` returns the two-bucket pipeline: pre-auth IP (30/60s, fires BEFORE the DB lookup so brute-force load against `access_tokens` is actually capped) + post-auth token-id (60/60s). Tracks `lastTouchedMs` separately from `lastRefillMs` so an exhausted key can't be reset by hammering past the TTL. LRU cap bounds memory under attacker-controlled key growth.
- `src/commands/serve-http.ts` (v0.26.0) — Express 5 HTTP MCP server with OAuth 2.1, admin dashboard, and SSE live activity feed. Started via `gbrain serve --http [--port N] [--token-ttl N] [--enable-dcr] [--public-url URL] [--log-full-params]`. Supersedes the v0.22.7 `src/mcp/http-transport.ts` simple bearer-auth path. Combines MCP SDK's `mcpAuthRouter` (authorize / token / register / revoke endpoints), a custom `client_credentials` handler (SDK's token endpoint throws `UnsupportedGrantTypeError` for CC; the custom handler runs BEFORE the router and falls through for `auth_code` / `refresh_token`), `requireBearerAuth` middleware for `/mcp` with scope enforcement before op dispatch, `localOnly` rejection, and `express-rate-limit` at 50 req / 15 min on `/token`. Serves the built admin SPA from `admin/dist/` with SPA fallback. `/admin/events` SSE endpoint broadcasts every MCP request to connected admin browsers. `cookie-parser` middleware wired (Express 5 has no built-in). Startup logging prints port, engine, configured issuer URL (honors `--public-url`), registered-client count, DCR status, and admin bootstrap token. **v0.26.9 hardening pass:** F7 sets `remote: true` explicitly on the `/mcp` request handler's OperationContext literal (closes the HTTP shell-job RCE — without this, `submit_job`'s protected-name guard at `operations.ts:1391` saw a falsy undefined and skipped, letting a `read+write`-scoped OAuth token submit `shell` jobs). F8 wires `summarizeMcpParams` from `src/mcp/dispatch.ts` into both `mcp_request_log` writes and the admin SSE feed by default (raw payloads opt-in via `--log-full-params` with stderr warning). F9 sets cookie `Secure` flag when behind HTTPS or a public-URL proxy. F10 caps the magic-link nonce store with an LRU bound. F12 routes DCR disable through the `GBrainOAuthProvider` constructor's `dcrDisabled` option instead of the prior monkey-patch on the express router. F14 wraps `transport.handleRequest` in try/catch so SDK throws return a JSON-RPC 500 envelope instead of express's default HTML error page. F15 unifies OperationError + unexpected exceptions through `buildError` / `serializeError` so `/mcp` always returns the same envelope shape. **v0.28.1:** `/health` endpoint extracted into pure `probeHealth(engine)` async function with `HEALTH_TIMEOUT_MS = 3000` exported constant — drops the timeout from 5s to 3s so Fly.io's 5s health-check deadline gets 2s of headroom for TCP, response framing, and clock skew. Races `engine.getStats()` against the timeout via `Promise.race`; saturated pool returns 503 with `Health check timed out (database pool may be saturated)` instead of hanging. `clearTimeout` in finally block prevents pending-timer pile-up under high probe rates (race-leak fix from adversarial review). **v0.28.10:** `/health` is now liveness-only via the new `probeLiveness(sql, engineName, version, timeoutMs)` helper that races `sql\`SELECT 1\`` against `HEALTH_TIMEOUT_MS` and returns the same `ProbeHealthResult` tagged-union as `probeHealth` (single timer-cleanup site, single 503 envelope). Body shape: `{status, version, engine}` only — engine stats are no longer spread on the public route. Full stats moved to a new admin endpoint `/admin/api/full-stats` (sibling to `/admin/api/stats` and `/admin/api/health-indicators`) gated by the existing `requireAdmin` middleware; that route calls `probeHealth(engine, ...)` and returns the original spread-stats body. `?full=true` query param removed entirely. Closes the original DoS surface where `getStats()`'s 6× count(*) on 96K-page brains through PgBouncer exceeded `HEALTH_TIMEOUT_MS` and triggered orchestrator restart cascades (Fly.io / k8s seeing 503 → restart loop → advisory-lock pile-up on the migration lock). Outside-voice review (Codex) caught that `/admin/api/health-indicators` is NOT a full-stats endpoint (returns only `{expiring_soon, error_rate}`), and that an alternative loopback-IP gate would have depended on `app.set('trust proxy', 'loopback')` semantics holding under proxy/XFF misconfiguration; the shipped admin-cookie design avoids both. **v0.31.3 (#681):** every OAuth/admin/audit SQL call routes through `sqlQueryForEngine(engine)` from `src/core/sql-query.ts` so `gbrain serve --http` works against PGLite brains. The four `mcp_request_log.params` INSERT sites (success path, auth_failed path, scope_denied path, server-error path) all go through `executeRawJsonb(engine, ...)` so the JSONB column stores real objects, not JSON-encoded strings — closes the bug where `params->>'op'` returned the encoded string `"search"` (with quotes) instead of `search`. Migration v46 normalizes any pre-v0.31.3 string-shaped backlog rows on first start. **v0.34.1.0 (#864):** new `--bind HOST` CLI flag with default `127.0.0.1`. Personal-laptop installs no longer publish the brain to the LAN by accident. Self-hosted operators pass `--bind 0.0.0.0` (or a specific interface IP) once to accept remote connections. A stderr WARN fires when `--public-url` is set without `--bind` so the operator sees the binding before the first request (common cause of "ngrok forwards to me but the agent can't reach the upstream" misconfigurations). The startup banner prints a `Bind:` line. **v0.34.1.0 (#861):** drops the `(authInfo as AuthInfo & {sourceId?: string}).sourceId ?? env ?? 'default'` cast chain — `AuthInfo.sourceId` and `AuthInfo.allowedSources` are now the typed source of truth, populated by `oauth-provider.ts:verifyAccessToken` from the `oauth_clients` row. **v0.35.3.0:** the inline ParamDef→schema mapper at `:837-849` (HTTP MCP `tools/list` handler) is replaced with `paramDefToSchema(v)` from `src/mcp/tool-defs.ts`. Pre-fix this site silently dropped `items` on every array param so strict-mode OAuth clients (Gemini Pro structured outputs, OpenAI strict tool defs) rejected the whole tool list. Single mapper now serves stdio MCP, HTTP MCP `tools/list`, and the subagent registry.
- `src/core/sql-query.ts` (v0.31.3) — Engine-aware tagged-template SQL adapter for OAuth/admin/auth infrastructure. `sqlQueryForEngine(engine)` returns a `SqlQuery` (`(strings, ...values) => Promise<rows[]>`) that walks the template, builds `$N` positional SQL, asserts every value is a `SqlValue` (string | number | bigint | boolean | Date | null), and routes through `engine.executeRaw(sql, params)` so Postgres goes via postgres.js's `unsafe(sql, params)` path and PGLite via its embedded `db.query(sql, params)`. Deliberately narrower than postgres.js's `sql` tag: no nested fragments, no `sql.json()`, no `sql.unsafe()`, no `sql.begin()`, no array binding. The narrow surface is the feature — codex finding #7 from the v0.31 plan review argued the adapter should stay scalar-only or it drifts into a partial postgres.js clone. JSONB writes go through the separate `executeRawJsonb(engine, sql, scalarParams, jsonbParams)` helper that composes positional `$N::jsonb` casts and passes JS objects through; the v0.12.0 double-encode bug class doesn't apply because positional binding through `unsafe()` reaches the wire protocol with the correct type oid (verified by `test/sql-query.test.ts` on PGLite and `test/e2e/auth-permissions.test.ts:67` on Postgres). `scripts/check-jsonb-pattern.sh` doesn't fire because `executeRawJsonb(...)` is a method call, not the banned literal-template-tag interpolation pattern. Consumed by `src/commands/auth.ts`, `src/commands/serve-http.ts`, `src/core/oauth-provider.ts`, `src/commands/files.ts`, and `src/mcp/http-transport.ts` so all five sites work against PGLite and Postgres uniformly. Closes the bug where `gbrain auth` + `gbrain serve --http` were silently Postgres-only because they routed every SQL through the postgres.js singleton (community PR #681).
- `src/commands/serve.ts` (v0.31.3) — `gbrain serve` stdio MCP entrypoint with idempotent shutdown across every parent-disconnect signal. Stdio EOF, SIGTERM, SIGINT, SIGHUP, and parent-process death (every reparent case — PID 1, launchd subreaper, systemd, tmux, or a parent shell with `PR_SET_CHILD_SUBREAPER`) all funnel into one `cleanup(reason)` path that releases the engine and the PGLite write-lock dir within 5 seconds. Pre-v0.31.3 the stdio MCP server held the lock indefinitely after Claude Desktop / Cursor / launchd-managed gateways disconnected, forcing a 5-minute stale-lock wait on the next start. Watchdog reparent check is `getParentPid() !== initialParentPid` (capturing the initial ppid once at install time and firing on any change); the previous `=== 1` check missed the subreaper case under launchd / systemd. Bun's `process.ppid` cache is stale across reparenting (see [oven-sh/bun#30305](https://github.com/oven-sh/bun/issues/30305)) so `getParentPid()` runs `spawnSync('ps', ['-o', 'ppid=', '-p', PID])` per tick to read the live kernel PPID. Startup probe verifies `ps` is on PATH; if not (stripped containers, busybox without procps), the watchdog skips installing AND emits a loud `[gbrain serve] watchdog disabled: ps unavailable, parent-death detection unavailable — child will rely on stdin EOF / signals only` stderr line so operators see the degraded mode at boot. Pinned by `test/serve-stdio-lifecycle.test.ts` (22 cases). Closes #413, #446. Credit @Aragorn2046 (origin features in #591) and @seungsu-kr (rebased submitter, Bun ppid workaround).
- `src/core/oauth-provider.ts` (v0.26.0) — `GBrainOAuthProvider` implementing the MCP SDK's `OAuthServerProvider` + `OAuthRegisteredClientsStore` interfaces. Backed by raw SQL (works on both PGLite and Postgres — OAuth is infrastructure, not a BrainEngine concern). Full OAuth 2.1 spec: `authorize` + `exchangeAuthorizationCode` with PKCE (for ChatGPT), `client_credentials` (for Perplexity / Claude), `refresh_token` with rotation, `revokeToken`, `registerClient` (DCR path validates redirect_uri must be `https://` or loopback per RFC 6749 §3.1.2.1). All tokens + client secrets SHA-256 hashed before storage. Auth codes single-use with 10-minute TTL via atomic `DELETE...RETURNING` (closes RFC 6749 §10.5 TOCTOU race). Refresh rotation also `DELETE...RETURNING` (closes §10.4 stolen-token detection bypass). `pgArray()` escapes commas/quotes/braces in elements so a comma-bearing redirect_uri can't smuggle a second array element. Legacy `access_tokens` fallback in `verifyAccessToken` grandfathers pre-v0.26 bearer tokens as `read+write+admin`. `sweepExpiredTokens()` runs on startup wrapped in try/catch. **v0.26.9 RFC 6749/7009 hardening pass:** F1+F2 fold `client_id` atomically into the `DELETE WHERE` clauses for both auth-code exchange and refresh rotation — pre-fix the post-hoc client compare burned the row on wrong-client paths so the legitimate client couldn't retry. F3 enforces refresh-scope-subset against the original grant on the row (RFC 6749 §6), not the client's currently-allowed scopes — fixes the case where revoking a scope from a client wouldn't shrink the agent's existing refresh tokens. F4 binds `client_id` on `revokeToken` so a client can only revoke its own tokens (RFC 7009 §2.1). F7c validates the `/token` request's `redirect_uri` against the value stored at `/authorize` (RFC 6749 §4.1.3) — empty-string treated as missing rather than wildcard match (adversarial-review fix). F5 swaps bare `catch {}` blocks in `verifyAccessToken` and `getClient` for `isUndefinedColumnError` from `src/core/utils.ts` — only SQLSTATE 42703 falls through to legacy fallback; lock timeouts and network blips throw and surface. F6 makes `sweepExpiredTokens()` actually return the count via `RETURNING 1` + array length, not a fire-and-forget zero. F12 adds `dcrDisabled` constructor option so `serve-http.ts` can disable the `/register` endpoint without monkey-patching the router. **v0.26.2:** module-private `coerceTimestamp()` boundary helper at the top of the file normalizes postgres-driver-as-string BIGINT columns to JS numbers at every read site (5 call sites: `getClient` L112+L113 for DCR `/register` RFC 7591 §3.2.1 numeric timestamps, `exchangeRefreshToken` L274 + `verifyAccessToken` L296+L303 for the SDK's `typeof === 'number'` bearerAuth check). Throws on non-finite input (NaN/Infinity) so corrupt rows fail loud at the boundary instead of riding through as `expiresAt: NaN`; returns undefined for SQL NULL so callers decide NULL semantics explicitly (refresh + access token paths treat NULL as expired). Helper intentionally NOT promoted to `src/core/utils.ts` — codex review flagged repo-wide BIGINT precision-loss risk for a generic helper. **v0.34.1.0 (#909):** `registerClient` honors `token_endpoint_auth_method: "none"` (RFC 7591 §3.2.1) — public PKCE clients (Claude Code, Cursor, every other PKCE-first MCP client) store `client_secret_hash = NULL` and the response payload omits `client_secret` entirely. Confidential clients (default `client_secret_post` and explicit `client_secret_basic`) keep their one-time-reveal shape. `getClient` correctly normalizes a NULL `client_secret_hash` to JS `undefined` so the SDK's clientAuth path accepts the public client at `/token`. **v0.34.1.0 (#861 + #876):** `verifyAccessToken` JOINs `oauth_clients.source_id` (write scope, scalar) + `oauth_clients.federated_read` (read scope, TEXT[]) and surfaces both on the returned `AuthInfo`. Pre-v60 / pre-v61 brains degrade gracefully via `isUndefinedColumnError` fallback so the upgrade chain is non-blocking on legacy DBs.
- `admin/` (v0.26.0) — React 19 + Vite + TypeScript admin SPA embedded in the binary via `admin/dist/` served by `serve-http.ts`. 7 screens: Login (bootstrap token → session cookie), Dashboard (metrics + SSE feed + token health), Agents (sortable table + sparklines + Register button), Register (modal with scope checkboxes + grant type selector), Credentials reveal (full-screen modal with Copy + Download JSON + yellow one-time-only warning), Request Log (filterable paginated), Agent Detail drawer (Details / Activity / Config Export tabs + Revoke). Design tokens: `#0a0a0f` bg, Inter for UI, JetBrains Mono for data, 4-32px spacing scale, rounded pill badges. HTTP-only SameSite=Strict cookie auth. 65KB gzip. Build: `cd admin && bun install && bun run build`; output at `admin/dist/` is committed for self-contained binaries.
- `src/commands/auth.ts` — Token management. `gbrain auth create/list/revoke/test` for legacy bearer tokens (v0.22.7 wired as a first-class CLI subcommand) plus `gbrain auth register-client` (v0.26.0) and `gbrain auth revoke-client <client_id>` (v0.26.2) for OAuth 2.1 client lifecycle. `revoke-client` runs an atomic `DELETE...RETURNING` on `oauth_clients`; FK `ON DELETE CASCADE` on `oauth_tokens.client_id` and `oauth_codes.client_id` purges every active token + authorization code in a single transaction. `process.exit(1)` on no-such-client (idempotent — re-running on the same id produces the same exit-1 message). Legacy tokens stored as SHA-256 hashes in `access_tokens`; OAuth clients in `oauth_clients`. As of v0.26.0, legacy tokens grandfather to `read+write+admin` scopes on the OAuth HTTP server, so pre-v0.26 deployments keep working with no migration. **v0.31.3 (#681):** every SQL site routes through `sqlQueryForEngine(engine)` from `src/core/sql-query.ts` (and `executeRawJsonb` for the takes-holders `permissions` JSONB column) so `gbrain auth` works against PGLite brains. Pre-fix, every call hit the postgres.js singleton via `getConn()` and silently failed (or wrote to the wrong DB) when the active engine was PGLite. The takes-holders write goes through `executeRawJsonb(engine, sql, [name, hash], [{takes_holders:[...]}])` which round-trips with `jsonb_typeof = 'object'` instead of the pre-v0.31.3 quoted-string shape. **v0.34.1.0 (#876):** `register-client` accepts `--source <id>` (write authority, scalar) and `--federated-read <S1,S2,...>` (read scope, array). The output prints the resolved `Write source` and `Federated reads` for the registered client. Pre-v0.34 clients backfill to `source_id='default'` via migration v60 so existing deployments keep their v0.33 effective behavior verbatim.
- `src/commands/upgrade.ts` — Self-update CLI. `runPostUpgrade()` enumerates migrations from the TS registry (src/commands/migrations/index.ts) and tail-calls `runApplyMigrations(['--yes', '--non-interactive'])` so the mechanical side of every outstanding migration runs unconditionally.
- `src/commands/migrations/` — TS migration registry (compiled into the binary; no filesystem walk of `skills/migrations/*.md` needed at runtime). `index.ts` lists migrations in semver order. `v0_11_0.ts` = Minions adoption orchestrator (8 phases). `v0_12_0.ts` = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify). `phaseASchema` has a 600s timeout (bumped from 60s in v0.12.1 for duplicate-heavy brains). `v0_12_2.ts` = JSONB double-encode repair orchestrator (4 phases: schema → repair-jsonb → verify → record). `v0_14_0.ts` = shell-jobs + autopilot cooperative (2 phases: schema ALTER minion_jobs.max_stalled SET DEFAULT 3 — superseded by v0.14.3's schema-level DEFAULT 5 + UPDATE backfill; pending-host-work ping for skills/migrations/v0.14.0.md). All orchestrators are idempotent and resumable from `partial` status. As of v0.14.2 (Bug 3), the RUNNER owns all ledger writes — orchestrators return `OrchestratorResult` and `apply-migrations.ts` persists a canonical `{version, status, phases}` shape after return. Orchestrators no longer call `appendCompletedMigration` directly. `statusForVersion` prefers `complete` over `partial` (never regresses). 3 consecutive partials → wedged → `--force-retry <version>` writes a `'retry'` reset marker. v0.14.3 (fix wave) ships schema-only migrations v14 (`pages_updated_at_index`) + v15 (`minion_jobs_max_stalled_default_5` with UPDATE backfill) via the `MIGRATIONS` array in `src/core/migrate.ts` — no orchestrator phases needed. **v0.41.37.0 (#1605):** new `in-process.ts` exports `runMigrateOnlyCore({timeoutMs?})` — the single source of truth for "bring schema to head" (`configureGateway` → `createEngine` → `connect` → `initSchema` → `disconnect`, idempotent, 600s wall-clock guard `MIGRATE_ONLY_TIMEOUT_MS`, throws `MigrateOnlyError` on no-config / timeout). The migration orchestrators' 9 schema phases AND `init.ts:initMigrateOnly` (the `gbrain init --migrate-only` CLI path) both delegate to it, so the schema bring-up can't drift between them. Previously each phase shelled out to a child `gbrain init --migrate-only` via `execSync`; on Windows + bun + Supabase pooler the SPAWNED child died with `getaddrinfo ENOTFOUND` before it could connect (a bun-on-Windows child-process DNS failure, NOT an env-propagation bug — the parent connects fine with `env: process.env`). Running in-process removes the spawn entirely. `runGbrainSubprocess` is the diagnostic wrapper for the REMAINING non-schema spawns (extract/repair/stats): captures child stderr (64MB buffer) and folds it into the thrown error so a Windows failure shows the real `getaddrinfo ENOTFOUND` line instead of a bare `Command failed`. Pinned by `test/migration-in-process.serial.test.ts`. **v0.41.37.0 (#1581):** `v0_13_1.ts:phaseCGrandfather` rewritten from a per-page `getPage` + `putPage` loop (which hung CPU-bound 70+ min on an 82K-page PGLite brain) to a CHUNKED bulk SQL pass. Three correctness properties the per-page loop and a naive single bulk UPDATE both got wrong: (1) keyed on `pages.id` (globally unique PK), NOT slug — slug uniqueness is `(source_id, slug)`, so a slug-batched UPDATE would mutate same-slug pages across other sources; (2) filters `deleted_at IS NULL` so tombstones aren't grandfathered; (3) chunked in `CHUNK_SIZE` batches (DELETE_BATCH_SIZE convention) so lock-hold stays bounded instead of one giant transaction. The rollback log carries source identity (`{id, slug, source_id, pre_frontmatter}`) so a rollback is unambiguous across sources. Idempotent + resumable (each UPDATE flips its rows out of `GRANDFATHER_WHERE`). Completes ~1-2s on the 82K-page brain. Pinned by `test/migrations-v0_13_1-grandfather.test.ts`.
- `src/commands/repair-jsonb.ts` — `gbrain repair-jsonb [--dry-run] [--json]`: rewrites `jsonb_typeof='string'` rows in place across 5 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter). Fixes v0.12.0 double-encode bug on Postgres; PGLite no-ops. Idempotent.
- `src/commands/orphans.ts` — `gbrain orphans [--json] [--count] [--include-pseudo] [--source <id>]`: surfaces pages with zero inbound wikilinks, grouped by domain. Auto-generated/raw/pseudo pages filtered by default. Also exposed as `find_orphans` MCP operation. Shipped in v0.12.3 (contributed by @knee5). **v0.41.29.0 source-scoping wave:** `findOrphans`/`getOrphansData` (the canonical pure fn shared with doctor's `orphan_ratio`) takes `{ sourceId?, sourceIds? }`; `BrainEngine.findOrphanPages(opts?)` (both engines) scopes ONLY the candidate side (`p.source_id = $1` scalar, or `= ANY($1::text[])` federated) while still counting inbound links from ANY source — a page in source X linked FROM source Y is reachable, so NOT an orphan of X (the deliberate, less-surprising definition; the stricter intra-source-only reading is rejected). `--source` is an explicit raw-flag parse (NOT `resolveSourceWithTier`, which would scope bare invocations to a default). Also corrected the `total_linkable` denominator: it now enumerates ALL live pages (scoped) and subtracts every excluded-by-slug page (templates/, scratch/, etc.) — pre-fix `total - excludedOrphans` left excluded NON-orphan pages with inbound links in the denominator, inflating it and suppressing warnings (changes orphan_ratio output for every brain, in the accurate direction). The `find_orphans` MCP op threads `sourceScopeOpts(ctx)` so a source-bound OAuth client no longer sees brain-wide orphans (closes a cross-source read leak in the v0.34.1 class). `gbrain doctor --source <id>` scopes `orphan_ratio` (entity-count gate + getOrphansData + messages) and, under explicit `--source` below 100 entity pages, reports the ratio with a low-scale caveat instead of a vacuous "ok". Thin-client `doctor --source` orphan_ratio remains brain-wide (TODO). Pinned by `test/orphans-source-scope.test.ts` (PGLite) + `test/e2e/engine-parity.test.ts` (Postgres↔PGLite scalar + federated parity).
- `src/commands/salience.ts` (v0.29) — `gbrain salience [--days N] [--limit N] [--kind PREFIX] [--json]`: pages ranked by emotional + activity salience over a recency window. Mirrors orphans.ts shape (pure data fn + JSON formatter + human formatter). Calls `engine.getRecentSalience(opts)`. Score formula: `(emotional_weight × 5) + ln(1 + active_take_count) + 1/(1 + days_since_update)`.
- `src/commands/anomalies.ts` (v0.29) — `gbrain anomalies [--since YYYY-MM-DD] [--lookback-days N] [--sigma N] [--json]`: cohort-level activity outliers. Calls `engine.findAnomalies(opts)`. Two cohort kinds in v1: tag, type. Year cohort deferred to v0.30.
- `src/commands/whoknows.ts` (v0.33) — `gbrain whoknows <topic> [--explain] [--limit N] [--json]`: expertise + relationship-proximity routing. Mirrors v0.29 salience/anomalies shape (pure `rankCandidates()` + `findExperts()` orchestrator + `runWhoknows()` CLI dispatch + thin-client routing). MCP op = `find_experts` (scope: read, localOnly: false) per ENG-D5. Ranking formula (ENG-D1 locked): `score = log(1 + raw_match) × max(0.1, exp(-days/180)) × (0.5 + 0.5 × salience)` where `raw_match` is hybridSearch's RRF+source-boost score. Filters at SQL via the new `SearchOpts.types: ['person', 'company']` (no post-filter waste). hybridSearch's internal salience+recency boosts are intentionally disabled — the locked formula applies on a clean signal. Floors prevent multiplicative-zero edge cases (cold-start people stay visible); ties break alphabetically by slug for determinism. 16 unit tests in `test/whoknows.test.ts` pin the math.
- `src/commands/eval-whoknows.ts` (v0.33, v0.33.1.3 thin-client wiring) — `gbrain eval whoknows <fixture.jsonl> [--json] [--skip-replay]`: two-layer eval gate (ENG-D2). Layer 1 quality (hand-labeled fixture, top-3 hit rate ≥ 0.8). Layer 2 regression (`eval_candidates` replay set-Jaccard@3 ≥ 0.4). Sparseness fallback: < 20 replay-eligible rows → Layer 2 auto-skips with stderr warning. Stable JSON envelope with `schema_version: 1`. Exit 0/1/2 for pass/fail/usage so CI can gate. Mirrors v0.27.x cross-modal + v0.28.1 longmemeval dispatch shape under `src/commands/eval.ts`. **v0.33.1.3:** `WhoknowsFn` callable abstraction lets the gates be impl-agnostic. `runEvalWhoknows(engine: BrainEngine | null, args)` picks the impl at entry — thin-client mode (`isThinClient(cfg)`) routes per-query through `callRemoteTool(cfg, 'find_experts', {topic, limit})` via the v0.31.1 seam; local mode calls `findExperts(engine, ...)` directly. cli.ts adds a thin-client bypass before `connectEngine` for `gbrain eval whoknows`, matching the longmemeval/cross-modal no-DB pattern. Regression gate auto-skips in thin-client mode (no DB access to `eval_candidates`). Public exports `jaccardAtK`, `topKHit`, `readFixture`, `WhoknowsFn`, threshold constants are pinned by `test/eval-whoknows.test.ts` (25 cases, +2 for the null-engine signature contract).
- `test/fixtures/whoknows-eval.jsonl` (v0.33) — 10-row synthetic placeholder demonstrating the eval-fixture schema (`{query, expected_top_3_slugs, notes?}` JSONL). End users replace with their own real queries before shipping; the placeholder uses obviously-example slugs (`wiki/people/example-alice`) so production data isn't conflated with the test fixture. Drives `test/e2e/whoknows.test.ts` (which seeds a matching synthetic brain and asserts the >=80% gate) and the `whoknows_health` doctor check.
- `src/core/brainstorm/{domain-bank,orchestrator,judges}.ts` + `src/commands/{brainstorm,lsd,eval-brainstorm}.ts` + `src/core/last-retrieved.ts` (v0.37.0 Open Collider wave) — bisociation-grounded idea generation pair: `gbrain brainstorm <question>` (defensible, cite-heavy, 4 close × 6 far, judge threshold 4.0/5, save by default) and `gbrain lsd <question>` (Lateral Synaptic Drift — inverted judge that rejects ideas with resistance >4.5 ("too obvious"), stale-page bias via `pages.last_retrieved_at`, 2 close × 12 far, axiomatic inversions required, ephemeral by default). The architecture corrects Open Collider's training-data-grounded approach: gbrain has the user's actual cross-domain knowledge already, so the "domain bank" is prefix-stratified sampling from the user's own brain (`SELECT DISTINCT substring(slug from '^[^/]+/[^/]+')` cached 1h-TTL in `config` table per source) tiebroken by `JOIN page_links` connection_count, with corpus-sampling fallback when fewer prefixes than M exist. Distance scores normalized to [0,1] via `1 - clamp(cosine_distance, 0, 2) / 2` (1=opposite, 0=identical). The judge is a single `judges.ts` with `runJudge(config, ideas)` + two exported configs (`BRAINSTORM_JUDGE_CONFIG` weighted originality/resistance/thesis_density/concrete_grounding/cognitive_load 0.25/0.20/0.20/0.20/0.15 vs `LSD_JUDGE_CONFIG` with cognitive_load 0.50 + inversion rule). Calibration cold-start fallback (D4 + codex #8): when `calibration_profiles.active_bias_tags` is empty, judge runs without anti-bias context AND stderr-warns. Op-layer write-back at `src/core/operations.ts` `search`/`query`/`get_page` handlers fires `bumpLastRetrievedAt(engine, pageIds)` (fire-and-forget, 5-min throttled via SQL clause, default-on with `search.track_retrieval` config escape hatch per D13) — internal callers (sync, migrations, dream cycle) bypass the op layer so the LSD stale signal stays clean. **v0.41.8.0 (#1247/#1269/#1290):** the IIFE is now tracked in a module-scoped `Set<Promise<unknown>>` (mirrors the v0.36.1.x `awaitPendingSearchCacheWrites` precedent for #1090). New exported `awaitPendingLastRetrievedWrites(timeoutMs?: number): Promise<{outcome, pending}>` resolves once all tracked promises settle, bounded by a 5s `Promise.race` timeout that stderr-warns with the pending count if it fires. `src/cli.ts` awaits the drain unconditionally for every op in the op-dispatch finally block BEFORE `engine.disconnect()`, then narrows a fallback `process.exit(0)` to fire ONLY when `outcome === 'timeout'` AND `shouldForceExitAfterMain(argv)` (excludes `serve` so daemons stay alive). Closes the PGLite CLI search/query/get-hang class: pre-fix, the IIFE raced disconnect, PGLite's WASM kept Bun's event loop alive, CLI hung at ~95-98% CPU until SIGKILL. Three community-validated reports; PR #1259 (jehoon) supplied the structural drain pattern; PR #1337 (matt-dean-git) supplied the snapshot+early-null disconnect pattern AND the force-exit guard we narrowed to fire only on the timeout path. Pinned by `test/last-retrieved.test.ts` (6 unit cases: empty/single/multi-pending settle, throw-in-IIFE still settles, permanently-pending hits timeout, empty pageIds untracked), `test/e2e/pglite-cli-exit.serial.test.ts` (IRON-RULE behavioral regression: real `bun src/cli.ts` subprocess against a hermetic PGLite tempdir, asserts search/get/query exit 0 in <15s + daemon-survival case), `test/fix-wave-structural.test.ts` (behavioral-positioning assertion that the drain `await` appears textually BEFORE `engine.disconnect` in the local-engine path — survives variable-rename refactors). Migration v79 adds `pages.last_retrieved_at TIMESTAMPTZ NULL` + full B-tree index (NOT partial — covers both NULL and range branches per codex r2 #6); full forward-reference bootstrap probe on both engines. Frontmatter `mode: lsd` makes the dream-cycle synthesize phase skip LSD output (noise-by-design — `isLsdOutput()` check in `src/core/cycle/transcript-discovery.ts` short-circuits `isDreamOutput()`). `gbrain eval brainstorm <fixture.jsonl>` is a three-axis evaluation gate (distance + usefulness + grounding, conjunctive) per codex r2 #11 — distance alone is gameable. `gbrain doctor` gains `brainstorm_health` check surfacing (a) migration v79 applied, (b) `search.track_retrieval` setting, (c) calibration cold-start status. 38 unit tests across `test/brainstorm/{distance,lsd-mode-skip,eval-brainstorm}.test.ts`. Plan: `~/.claude/plans/system-instruction-you-are-working-staged-coral.md`. Open Collider source: `github.com/CL-ML/open-collider`. **v0.41.21.0:** judges.ts replaces `maxTokens: 4000` with `computeJudgeMaxTokens(ideaCount, modelId)`. Named constants at top of file: `TOKEN_BUDGET_PER_IDEA`, `TOKEN_BUDGET_ENVELOPE`, `LEGACY_MIN_MAX_TOKENS`, `MAX_OUTPUT_TOKENS_CEIL`. New `ANTHROPIC_OUTPUT_CAPS` map (Opus 4.7 = 32K, Sonnet 4.6 / Haiku 4.5 = 64K, legacy Claude 3.5 = 8K) so legacy 8K-cap models bind at 8K instead of failing mid-judge. When the caller passes no `modelOverride`, the cap routes through the gateway's actual configured chat model via `getChatModel()` so the formula matches what `chat()` will use (not whatever a stale override hints at). Closes the headline v0.41.21.0 bug: pre-fix, a 72-idea brainstorm chunked the judge into ~3 calls of ~24 ideas each; each call needed ~7.2K output tokens; the hard-coded 4K cap truncated every call mid-JSON; the parser threw; the whole run came back `judge_failed: true` with 0/72 scored. Post-fix: same fixture returns ~39/72 passing. Pinned by 16 cases in `test/brainstorm/judges-maxtokens.test.ts`. **v0.41.30.0:** `--save` for both `brainstorm` and `lsd` rewritten to persist through the canonical ingestion path instead of the lightweight DB-only write that never produced the advertised `.md` file. New exported `persistSavedIdea(engine, {slug, content, provenanceVia})` calls `importFromContent({noEmbed:true, sourcePath})` (chunked + tagged + content_hash so `gbrain search` finds the idea; no embedding cost at save time) THEN renders the saved row to disk via the shared `writePageThrough` helper (see `src/core/write-through.ts`) — file rendered FROM the row so the two sinks can't diverge and a later `gbrain sync` doesn't churn it. New exported pure `formatSaveOutcome(outcome, ctx)` returns an honest per-branch message: both-sinks success, DB-only (no `sync.repo_path` / repo-not-a-dir → file write skipped, exit 0), DB-saved-but-file-errored (exit 0, sync reconciles), and the total-failure case (neither sink → loud `save FAILED … NOT persisted` on stderr + nonzero exit). Closes the silent-false-success bug class where `--save` printed "Saved" unconditionally even when the PgBouncer-transaction-mode DB write failed and `gbrain get <slug>` then returned `page_not_found`. `buildIdeaSlug(question, label, nonce?)` gains a random nonce suffix (injectable for deterministic tests) so two same-day runs whose questions share the first 60 slug chars no longer clobber each other's page + file. `--json` callers stay DB-only (unchanged). New exported `buildBrainstormFrontmatterObject(result)` in orchestrator.ts returns the object form for `serializeMarkdown` (the string `buildBrainstormFrontmatter` is left untouched). Pinned by `test/brainstorm/save.test.ts` (covers `persistSavedIdea` both-sinks / DB-only / total-failure paths, `formatSaveOutcome` per-branch messages + exit codes, and `buildIdeaSlug` nonce collision-resistance).
- `src/core/write-through.ts` (v0.41.30.0, NEW) — shared atomic disk write-through for the canonical ingestion path. `writePageThrough(engine, slug, {sourceId?, frontmatterOverrides?, logger?})` reads `sync.repo_path`, re-reads the just-written DB row (`getPage`), renders it via `serializePageToMarkdown` + `resolvePageFilePath`, and writes the `.md` under the repo so the brain has a committable artifact that round-trips through `gbrain sync`. Rendering FROM the row means the file and the DB row cannot diverge. Extracted from the v0.38 `put_page` write-through in `src/core/operations.ts` (which the op now calls instead of hand-rolling its own copy) AND upgraded to ATOMIC: writes to a unique temp sibling (`<file>.tmp.<pid>.<rand>`) + `renameSync` into place, cleaning up the temp on any failure, so a crash or a concurrently-running `gbrain sync`/autopilot walking the live git tree can never read a half-written `.md` (matches the `.tmp + rename` convention in import-checkpoint.ts / op-checkpoint.ts). Never throws — returns `WriteThroughResult { written, path?, skipped?: 'no_repo_configured' | 'repo_not_found' | 'page_not_found_after_write', error? }` so the caller decides messaging + exit codes. Trust gating (subagent sandbox, dry-run) stays at the CALLER. Consumers: `put_page` op (write-through behavior preserved, now atomic) and `gbrain brainstorm/lsd --save` via `persistSavedIdea`. Pinned by `test/write-through.test.ts` (no-repo / repo-not-found / page-not-found-after-write skips, atomic-rename happy path + no stray `.tmp` on write failure, frontmatter-override stamping).
- `src/core/model-id.ts` (v0.41.21.0, NEW) — `splitProviderModelId(input: string | null | undefined): {provider: string | null, model: string}` shared parser for the pricing side. Splits on `:` first, then `/`. Defensive contract: null/undefined/empty/whitespace returns `{provider: null, model: ''}`. Five sites consume it (`src/core/anthropic-pricing.ts:estimateMaxCostUsd`, `src/core/budget/budget-tracker.ts:lookupPricing`, `src/core/eval-contradictions/cost-tracker.ts:pricingFor`, `src/core/minions/batch-projection.ts` at two call sites, `src/core/model-config.ts:isAnthropicProvider`) so the pricing + classification surface no longer has 5 parallel re-implementations of `provider:model` splitting. Closes the bug class where slash-form ids (`anthropic/claude-sonnet-4-6` — the form CLI flags accept and OpenRouter recipes emit) silently fell through to "unknown model" at every site. Distinct from the existing gateway-side `parseModelId` in `src/core/ai/model-resolver.ts`: that one throws on bare names because routing needs an explicit provider; this one returns `{provider: null, model: 'bare'}` because pricing lookups happen against bare model ids. Pinned by 16 cases in `test/model-id.test.ts`.
- `src/core/ai/model-resolver.ts:parseModelId` extension (v0.41.21.0) — gateway-side resolver extended to accept slash form alongside colon. Pre-fix the colon-only check threw `AIConfigError: model id must be in format provider:model` at every gateway entry point (chat / embed / rerank) the moment a slash-form id was passed. So even with the v0.41.21.0 pricing fix, a `--judge-model anthropic/claude-sonnet-4-6` invocation would clear BudgetTracker but then fail mid-judge inside `gateway.chat()`. Now both shapes resolve to the same recipe. Bare names without ANY separator still throw — gateway routing always needs an explicit provider. Pinned by 10 cases in `test/ai/model-resolver-slash.test.ts` including a `resolveRecipe` round-trip asserting slash form resolves to the same recipe object as colon form.
- `src/commands/transcripts.ts` (v0.29) — `gbrain transcripts recent [--days N] [--full] [--json]`: recent raw `.txt` transcripts from the dream-cycle corpus dirs. Imports `listRecentTranscripts` from `src/core/transcripts.ts` (the same library the gated `get_recent_transcripts` MCP op uses). Local-only by construction — the CLI always runs with `ctx.remote=false`.
- `src/commands/integrity.ts` — `gbrain integrity check|auto|review|extract`: bare-tweet detection, dead-link detection, three-bucket repair (auto-repair / review-queue / skip). `scanIntegrity()` is the shared library function called from `gbrain doctor` (sampled at limit=500) and `cmdCheck` (full scan). v0.22.8: batch-load fast path on Postgres uses a single SQL query to fix the PgBouncer round-trip timeout (60s → ~6s). Gated by `engine.kind === 'postgres'` at the call site so PGLite never enters batch; fallback `catch` logs at `GBRAIN_DEBUG=1` so real Postgres errors are diagnosable. **v0.32.8 (PR #860):** batch projection switched from `SELECT DISTINCT ON (slug)` to `SELECT ... ORDER BY source_id, slug` so multi-source brains scan each `(source, slug)` row independently (pre-fix the DISTINCT collapsed same-slug-different-source pages into one scan, the same bug class this PR fixes). Sequential and auto-repair loops use `listAllPageRefs()` to enumerate `(slug, source_id)` pairs and thread `sourceId` to `getPage`. Batch + sequential paths now report the same page count on multi-source brains.
- `src/commands/doctor.ts` — `gbrain doctor [--json] [--fast] [--fix] [--dry-run] [--index-audit]`: health checks. v0.12.3 added `jsonb_integrity` + `markdown_body_completeness` reliability checks. v0.14.1: `--fix` delegates inlined cross-cutting rules to `> **Convention:** see [path](path).` callouts (pipes DRY violations into `src/core/dry-fix.ts`); `--fix --dry-run` previews without writing. v0.14.2: `schema_version` check fails loudly when `version=0` (migrations never ran — the #218 `bun install -g` signature) and routes users to `gbrain apply-migrations --yes`; new opt-in `--index-audit` flag (Postgres-only) reports zero-scan indexes from `pg_stat_user_indexes` (informational only, no auto-drop). v0.15.2: every DB check is wrapped in a progress phase; `markdown_body_completeness` runs under a 1s heartbeat timer so 10+ min scans are observable on 50K-page brains. v0.19.1 added `queue_health` (Postgres-only) with two subchecks: stalled-forever active jobs (started_at > 1h) and waiting-depth-per-name > threshold (default 10, override via `GBRAIN_QUEUE_WAITING_THRESHOLD`). Worker-heartbeat subcheck intentionally deferred to follow-up B7 because it needs a `minion_workers` table to produce ground-truth signal. Fix hints point at `gbrain repair-jsonb`, `gbrain sync --force`, `gbrain apply-migrations`, and `gbrain jobs get/cancel <id>`. v0.22.12 (#500): `sync_failures` check shows `[CODE=N, ...]` breakdown for both unacked entries (warn) and acked-historical entries (ok), surfacing systemic failure modes (`SLUG_MISMATCH=2685`) instead of a bare count. v0.26.7 (#612): `rls_event_trigger` check (post-install drift detector for migration v35's auto-RLS event trigger). Lives outside the `// 5. RLS` slice that the structural doctor.test.ts guards anchor on, so the existing test guards stay intact. Healthy `evtenabled` set is `('O','A')` only — `R` is replica-only and would not fire in normal sessions; `D` is disabled. Fix hint is `gbrain apply-migrations --force-retry 35`. **v0.30.2:** `queue_health` gains a fourth subcheck — surfaces dead-lettered subagent jobs with `last_error` matching the `prompt_too_long` classifier within the last 24h. Fix hint points at `gbrain dream --phase synthesize --dry-run --json` to identify the offending transcript and `gbrain jobs prune --status dead --queue default` to clean up. Postgres-only. **v0.31.7:** `runDoctor` switches to `autoDetectSkillsDirReadOnly` (from `src/core/repo-root.ts`) so `bun install -g github:garrytan/gbrain && cd ~ && gbrain doctor` finds the bundled `skills/` via the install-path fallback instead of warning "Could not find skills directory" + docking the health score. `--fix` carries a D6 safety gate: when `detected.source === 'install_path'`, the command refuses auto-repair with a stderr message pointing at `$GBRAIN_SKILLS_DIR` / `$OPENCLAW_WORKSPACE` / `--skills-dir`, because `autoFixDryViolations` writes to SKILL.md files and would otherwise silently rewrite the install tree. The `graph_coverage` check now short-circuits to `ok: 'No entity pages — graph_coverage not applicable (markdown-only brain)'` when `SELECT COUNT(*) FROM pages WHERE type IN ('entity','person','company','organization')` returns 0 (closes #530); the entity count is woven into the warn message and the WARN hint switches from the long-deprecated `gbrain link-extract && gbrain timeline-extract` (gone since v0.16) to the canonical `gbrain extract all`. Pinned by an IRON-RULE regression assertion in `test/doctor.test.ts` that bans the stale verb names from the source string. **v0.32.4:** new `sync_freshness` check (exported `checkSyncFreshness` at the same file) added to both `runDoctor` (local) and `doctorReportRemote` (thin-client). Pure staleness probe — queries `sources.last_sync_at` only, no filesystem access. Warns at 24h, fails at 72h (or never-synced). Future-`last_sync_at` warns ("clock skew or corrupted timestamp") instead of silently falling through as ok — codex outside-voice caught the negative-ageMs bug pre-merge. Env-var overrides `GBRAIN_SYNC_FRESHNESS_WARN_HOURS` / `GBRAIN_SYNC_FRESHNESS_FAIL_HOURS`; invalid values fall back to defaults with a once-per-process stderr warn (`_resolveSyncFreshnessHours`). Failure messages embed `source.id` (not `source.name`) so the printed fix command `gbrain sync --source <id>` matches what the user copy-pastes. Filesystem-vs-DB page drift detection was deliberately stripped from the v0.32.4 scope — `doctorReportRemote` runs in the HTTP MCP server (`src/commands/serve-http.ts`), and walking DB-supplied `local_path` from a remote-callable endpoint crosses a trust boundary (OAuth write scope could mutate `sources.local_path`). Drift detection will resurface in a separate PR routed through `multi_source_drift`'s existing guard infrastructure (`GBRAIN_DRIFT_LIMIT` / `GBRAIN_DRIFT_TIMEOUT_MS`) with slug normalization tests and a meta-file allow-list. Pinned by 12 cases in `test/doctor.test.ts` ("v0.32.4 — sync_freshness check" describe block): empty sources, never-synced fail, >72h fail, exact 72h boundary, 24h-72h warn, exact 24h boundary, <24h ok, future-timestamp warn, mixed sources (highest severity wins), `executeRaw` throws → outer-catch warn, `GBRAIN_SYNC_FRESHNESS_FAIL_HOURS=6` override fires at 7h, source.id-in-message regression. **v0.36.3.0:** new `embedding_column_registry` check probes each declared column via Postgres `format_type(atttypid, atttypmod)` so a registry entry claiming 1024d Voyage against an actual 1536d OpenAI column surfaces with a paste-ready `gbrain config set embedding_columns '{...}'` ALTER hint instead of mysterious "vector dimension mismatch" errors at search time. On Postgres the check also probes HNSW index presence (`pg_indexes` lookup keyed by column name) and warns when missing (search will still work via seq scan but won't hit the index). The active default column's population coverage is computed via `COUNT(*) FILTER (WHERE <col> IS NOT NULL) / COUNT(*)` and warns below 90% — except empty brains (chunk_count = 0) where the gate short-circuits to `ok` so fresh `gbrain init` runs don't see "Active column 'embedding' is 0.0% populated" (CDX-5 codex fix). PGLite parity via the same SQL through `executeRaw` — registry validation happens on both engines. **v0.35.5.0:** the Lane D supervisor check at `doctor.ts:1011-1043` now consumes `summarizeCrashes(events)` from `src/core/minions/handlers/supervisor-audit.ts` instead of the pre-fix `events.filter(e => e.event === 'worker_exited').length`. The warn threshold drops from `>3` to `>=1` (any real crash is signal now that the counter is calibrated against clean exits). The ok message gains `clean_exits_24h=N`; the warn message gains `runtime=A oom=B unknown=C legacy=D` per-cause breakdown so an operator triages OOM vs runtime-error vs unknown-future-cause at a glance without grep'ing the JSONL audit. Closes the "Supervisor crashes: 120x/24h, was 62x — nearly doubled" alarm class that bit users on healthy brains after v0.34.3.0's RSS-watchdog work added more code=0 worker drains — both `doctor` and `gbrain jobs supervisor status` were counting every `worker_exited` event as a crash regardless of cause. Cross-surface parity is the regression guard: 4 source-grep wiring assertions in `test/doctor.test.ts` ban the ad-hoc filter pattern, pin the `>=1` threshold, and require the per-cause breakdown substrings (`runtime=`, `oom=`, `unknown=`, `legacy=`, `clean_exits_24h=`, `crashes_by_cause`) to appear in BOTH `doctor.ts` and `jobs.ts`. **v0.37.1.0:** new `skill_brain_first` check. Walks every SKILL.md under the configured skills dir (`autoDetectSkillsDirReadOnly` so `cd ~ && gbrain doctor` finds the bundled skills via the install-path fallback), calls `analyzeSkillBrainFirst()` from `src/core/skill-brain-first.ts` per file, aggregates verdicts into a single check with structured `Check.issues[]` for JSON tooling. Warn states: `missing_brain_first` (external-lookup pattern present, no canonical callout, no `brain_first: exempt`), `brain_first_typo` (near-miss declaration like `brain-first` or `BrainFirst` — paste-ready hint surfaces the correct snake_case form). Ok states: `compliant_callout`, `compliant_phase`, `compliant_position`, `exempt_frontmatter`, `no_external`. `--fix` routes through `dry-fix.ts` MISSING_RULE_PATTERNS to auto-insert the canonical `> **Convention:** see [conventions/brain-first.md](...)` callout (D6 install-path safety gate enforced — `--fix` from `~` refuses to write to the bundled tree). Snapshot+diff audit at `~/.gbrain/audit/skill-brain-first-YYYY-Www.jsonl` records detected / resolved / fixed transitions only (stable brains: 0 lines/run). Motivated by the 2026-05-19 tweet-shield incident: cross-modal eval flagged Garry's Palantir tweet as risky because no model knew he built it, but the brain already had "designed the entire Finance product UI" and "150+ PSDs from April-December 2006." Static check catches the AUTHORSHIP miss class; v0.37+ runtime gate (filed in TODOS.md) closes the dispatch side. **v0.41.27.0:** `checkSyncFreshness` gains a `localOnly`-gated git short-circuit (D4 trust-boundary preservation per Codex P0-1): `runDoctor` passes `localOnly: true`, `doctorReportRemote` keeps the default `false` so the HTTP MCP path doesn't walk DB-supplied `local_path` values via subprocess. The narrowed predicate (D7) mirrors sync.ts:1057+1075's actual "do work?" gate: HEAD == `last_commit` AND working tree clean AND `sources.chunker_version === String(CHUNKER_VERSION)`. Inline SELECT widens to carry `last_commit + chunker_version` (columns already exist; no schema migration). Three-bucket count math (D6) populates `Check.details = {unchanged_count, synced_recently_count, stale_count}` with the invariant `sum === sources.length` pinned in the test suite. OK message reshape (D2): all-unchanged → "All N up to date (no new commits since last sync)"; mixed → "N source(s): X synced recently, Y unchanged since last sync"; all-synced-recently keeps the prior message verbatim. `checkCycleFreshness` is INTENTIONALLY NOT touched (Codex P0-2 / D5): `last_commit == HEAD` answers "are there new commits to sync?" but cannot answer "did the full cycle complete?" — a sync can succeed while later cycle phases fail, and silencing that warn would hide real cycle staleness. Pinned by 9 new cases in `test/doctor.test.ts` ("v0.41.27.0 — sync_freshness git short-circuit" describe block) including a load-bearing D4 regression guard that verifies probes are NEVER called when `localOnly` is unset or false, plus the three-bucket invariant explicitly asserted in the mixed 3-source case. Supersedes PR #1564 (Co-Authored-By preserved). **v0.41.32.0 (supersedes #1623):** `checkSyncFreshness` short-circuit now passes `requireCleanWorkingTree: 'ignore-untracked'` (was `true`) — the headline fix: a quiet repo whose only dirt is untracked dirs is `unchanged`, not SEVERE. The SELECT widens to carry `newest_content_at`; the REMOTE (non-`localOnly`) path computes lag via `lagFromContentMs(newest_content_at, lastSync, now)` from the stored column — NO git subprocess on a DB-supplied `local_path` (trust boundary intact). LOCAL fall-through and the `< 0` clock-skew check stay on raw wall-clock (A1). `checkCycleFreshness` deliberately NOT content-relativized (CM2 — different axis, `last_full_cycle_at`; filed in TODOS as a probe-phase follow-up). Pinned by the "v0.41.32.0 — commit-relative staleness" describe in `test/doctor.test.ts` (T1 untracked-folders headline bug + T2/T2b/T2c remote-never-shells-out trust boundary).
- `src/core/migrate.ts` — schema-migration runner. Owns the `MIGRATIONS` array (source of truth for schema DDL). **v40 (v0.29):** `pages_emotional_weight` adds `pages.emotional_weight REAL NOT NULL DEFAULT 0.0`. Column-only (no index). On Postgres 11+ and PGLite, `ADD COLUMN` with a constant DEFAULT is metadata-only — instant on tables of any size. v0.14.2 extended the `Migration` interface with `sqlFor?: { postgres?, pglite? }` (engine-specific SQL overrides `sql`) and `transaction?: boolean` (set to false for `CREATE INDEX CONCURRENTLY`, which Postgres refuses inside a transaction; ignored on PGLite since it has no concurrent writers). Migration v14 (fix wave) uses a handler branching on `engine.kind` to run CONCURRENTLY on Postgres (with a pre-drop of any invalid remnant via `pg_index.indisvalid`) and plain `CREATE INDEX` on PGLite. v15 bumps `minion_jobs.max_stalled` default 1→5 and backfills existing non-terminal rows. v0.22.6.1: migration v24 (`rls_backfill_missing_tables`) uses `sqlFor: { pglite: '' }` to no-op on PGLite — PGLite has no RLS engine and is single-tenant by definition, and the v24 ALTERs target subagent tables that don't exist in pglite-schema.ts. Closes #395 (contributed by @jdcastro2). **v30 (v0.23):** creates `dream_verdicts (file_path TEXT, content_hash TEXT, worth_processing BOOL, reasons JSONB, judged_at TIMESTAMPTZ, PK(file_path, content_hash))`. RLS-enabled when running as a BYPASSRLS role. The synthesize phase reads/writes this table to avoid re-judging on backfill re-runs. **v35 (v0.26.7):** auto-RLS event trigger + one-time backfill. `auto_rls_on_create_table` fires on `ddl_command_end` for `WHEN TAG IN ('CREATE TABLE','CREATE TABLE AS','SELECT INTO')` and runs `ALTER TABLE … ENABLE ROW LEVEL SECURITY` on every new `public.*` table — no FORCE (matches v24/v29/schema.sql posture so non-BYPASSRLS apps can still read their own tables). The same migration backfills RLS on every existing `public.*` base table whose comment doesn't match the doctor regex (`^GBRAIN:RLS_EXEMPT\s+reason=\S.{3,}`). Per-table failure aborts the offending CREATE TABLE (event triggers fire inside the DDL transaction); no EXCEPTION wrap — that would convert loud rollback into silent permissive default. PGLite no-op via `sqlFor.pglite: ''`. Breaking change: operators with intentionally-RLS-off public tables must add the GBRAIN:RLS_EXEMPT comment BEFORE upgrade or the backfill will flip them on. **v46 (v0.31.3):** `mcp_request_log_params_jsonb_normalize` rewrites pre-v0.31.3 rows where `mcp_request_log.params` was stored as a JSON-encoded string (`jsonb_typeof = 'string'`) up to a real JSONB object via `UPDATE ... SET params = params::text::jsonb WHERE jsonb_typeof(params) = 'string'`. Single statement, idempotent — second-run finds no string-shaped rows and is a no-op. Closes the bug where `/admin/api/requests` returned a quoted string instead of the parsed object. **v0.36.3.0 (v68):** `eval_candidates_embedding_column` adds `eval_candidates.embedding_column TEXT NULL`. Per-row provenance for `gbrain eval replay`: captured rows record which column the live query ran against so replay reproduces the same retrieval space (Voyage rows replay against Voyage; OpenAI rows against OpenAI). NULL-tolerant — pre-v0.36 rows fall back to the current default during replay rather than failing. Column-only migration, metadata-only on both engines. **v0.34.1.0 (#861 + #876, v60-v65):** six-migration chain wires source-scoping into the OAuth client table. v60 (`oauth_clients_source_id_fk`) adds `oauth_clients.source_id TEXT` with NULL→`'default'` backfill and an FK to `sources(id) ON DELETE SET NULL`. v61 (`oauth_clients_federated_read_column`) adds `federated_read TEXT[] NOT NULL DEFAULT '{}'`. v62 (`oauth_clients_federated_read_backfill`) explicit-CASE backfills so `source_id IS NULL` produces `'{}'` not an array-containing-NULL. v63 (`oauth_clients_federated_read_validate`) is the fail-loud check that every row's source_id is in its federated_read array post-backfill. v64 (`oauth_clients_source_id_fk_restrict`) flips the FK to `ON DELETE RESTRICT` now that federated_read provides the alternative scope-loss path — source delete is refused if any client references it. v65 (`oauth_clients_federated_read_gin_index`) is the GIN index for the array-containment queries the read paths run. PGLite parity via `sqlFor.pglite` where needed. **v108 (v0.41.31.0):** `pages_embedding_signature` adds `pages.embedding_signature TEXT NULL` = `<provider:model>:<dims>` stamped when a page's chunks are embedded (`setPageEmbeddingSignature`). A later model/dimension swap makes the stored signature differ from the current one so `countStaleChunks`/`sumStaleChunkChars` (with the `signature` opt) and `invalidateStaleSignatureEmbeddings` can detect and re-embed those pages. GRANDFATHER (critical): the stale predicate is `embedding_signature IS NOT NULL AND embedding_signature <> $current`, so a NULL signature is NEVER stale — after this migration every existing page has NULL, none are flagged, and the next `embed --stale` does NOT re-embed the whole corpus. Signatures only get stamped going forward. No index (read only via a JOINed pages row in the chunk-grain stale queries; no standalone lookup hot path). `ADD COLUMN` with no DEFAULT (NULL) is metadata-only on Postgres 11+ / PGLite 17.5. **v109 (v0.41.32.0, supersedes #1623):** `sources_newest_content_at` adds `sources.newest_content_at TIMESTAMPTZ` — durable newest-COMMIT timestamp (HEAD committer time) written at sync time by `writeSyncAnchor`. The REMOTE staleness path (federation_health, get_status_snapshot MCP op) reads it instead of shelling out to git on a DB-supplied local_path. Renumbered 108→109 on the master merge that landed v0.41.31 pages_embedding_signature at v108. Metadata-only ADD COLUMN; mirror in pglite-schema.ts + schema.sql + bootstrap probe coverage. **v0.41.34.0 (retrieval-maxpool incident, v110 + v111):** v110 (`page_aliases`) creates the free-text alias table — `(id, source_id, alias_norm, slug, ...)` with `UNIQUE (source_id, alias_norm, slug)` and lookup indexes on `(source_id, alias_norm)` + `(source_id, slug)`. `alias_norm` is the output of `normalizeAlias()` so the WRITE side (ingest projection) and READ side (search) key on the same normalized form. Also lands in `src/core/pglite-schema.ts` for fresh PGLite installs. v111 (`search_telemetry_rank1_columns`) is `ADD COLUMN IF NOT EXISTS` on both engines for the rank-1 base_score drift signal: `sum_rank1_score`, `count_rank1`, and three coarse distribution buckets (`rank1_lt_solid` / `rank1_solid` / `rank1_high`) on the existing `search_telemetry` rollup — aggregate columns (NOT per-query rows, D10) so a downward drift in the median rank-1 match score is computable with bounded growth. `search_telemetry` lives only in migration v57, so these ALTER right after v57 runs.
- `src/core/progress.ts` — Shared bulk-action progress reporter. Writes to stderr. Modes: `auto` (TTY: `\r`-rewriting; non-TTY: plain lines), `human`, `json` (JSONL), `quiet`. Rate-gated by `minIntervalMs` and `minItems`. `startHeartbeat(reporter, note)` helper for single long queries. `child()` composes phase paths. Singleton SIGINT/SIGTERM coordinator emits `abort` events for every live phase. EPIPE defense on both sync throws and stream `'error'` events. Zero dependencies. Introduced in v0.15.2. **v0.40.3.0:** `emitHumanLine` is prefix-aware — when called inside a `withSourcePrefix(id, ...)` scope from `src/core/console-prefix.ts`, prepends `[id] ` to the line content. TTY-rewrite mode (`\r\x1b[2K`) gets the prefix inside the clear-to-EOL escape so the rewritten line carries the prefix too. JSON mode (`emitJson`) is intentionally NOT prefixed — NDJSON consumers parse the JSON envelope and would choke on a `[id] {...}` shape.
- `src/core/console-prefix.ts` (v0.40.3.0) — `AsyncLocalStorage<string>`-backed per-source line-prefix helper. Exports `withSourcePrefix(id, fn)` (runs `fn` with `id` as the active prefix; nested wraps replace the active prefix and restore on exit), `getSourcePrefix()` (read-only accessor; test seam), and `slog(...)` / `serr(...)` (prefix-aware `console.log` / `console.error` replacements). Embedded-newline-safe: a multi-line string under prefix `[foo]` emits `[foo] line1\n[foo] line2`. Outside a wrap, `slog` / `serr` fall through to bare `console.log` / `console.error` so single-source callers see identical output (back-compat invariant). Use `src.id` (slug-validated by `sources add`) NOT `src.name` (free-form text) to defeat log-injection through newline / control-character names. Coverage in v0.40.3.0: `src/commands/sync.ts` performSync + in-file callees (38 call sites migrated), `src/commands/embed.ts` runEmbedCore + helpers (16 call sites), `src/core/progress.ts` emitHumanLine. Lines emitted from outside these modules will NOT get the prefix under parallel sync — file an issue if you find a missed migration target.
- `src/core/cli-options.ts` — Global CLI flag parser. `parseGlobalFlags(argv)` returns `{cliOpts, rest}` with `--quiet` / `--progress-json` / `--progress-interval=<ms>` stripped. `getCliOptions()` / `setCliOptions()` expose a module-level singleton so commands reach the resolved flags without parameter threading. `cliOptsToProgressOptions()` maps to reporter options. `childGlobalFlags()` returns the flag suffix to append to `execSync('gbrain ...')` calls in migration orchestrators. `OperationContext.cliOpts` extends shared-op dispatch for MCP callers.
- `src/core/db-lock.ts` (v0.22.13) — generic `tryAcquireDbLock(engine, lockId, ttlMinutes)` over the existing `gbrain_cycle_locks` table. Parameterized lock id so different scopes can nest cleanly: `gbrain-cycle` for the broad cycle (held by `cycle.ts`) and `gbrain-sync` (`SYNC_LOCK_ID` constant) for `performSync`'s narrower writer window. Same UPSERT-with-TTL semantics as the prior cycle-only helper, just generalized. Survives PgBouncer transaction pooling (unlike session-scoped `pg_try_advisory_lock`); crashed holders auto-release once their TTL expires.
- `src/core/sync-concurrency.ts` (v0.22.13) — single source of truth for the parallel-sync policy. Exports `autoConcurrency(engine, fileCount, override?)` (PGLite always serial; explicit override clamped to >=1; auto path returns `DEFAULT_PARALLEL_WORKERS=4` when `fileCount > AUTO_CONCURRENCY_FILE_THRESHOLD=100`), `shouldRunParallel(workers, fileCount, explicit)` (Q1: explicit `--workers` bypasses the >50-file floor), and `parseWorkers(s)` (rejects `'0'`, `'-3'`, `'foo'`, `'1.5'`, trailing chars — replaces the prior parseInt-with-no-validation in both `sync.ts` and `import.ts`). Used by `performSync`, `performFullSync`, `runImport`, and the Minion `sync` handler so the three sites can no longer drift. **v0.40.3.0:** new sibling constant `DEFAULT_PARALLEL_SOURCES = 4` for the per-source fan-out under `gbrain sync --all`. Kept SEPARATE from `DEFAULT_PARALLEL_WORKERS` because they cover two different axes: total live Postgres connections per fan-out wave is approximately `DEFAULT_PARALLEL_SOURCES × DEFAULT_PARALLEL_WORKERS × 2 (per-worker pool)` = 32 connections with both at the default 4. Conflating them as one constant was a v0.40.2 footgun that Codex flagged during the v0.40.3.0 plan review; keeping them separate makes the multiplication visible at the constant level. The `× 2 per-file pool` factor is because each per-file worker opens its own `PostgresEngine` with `poolSize = min(2, resolvePoolSize(2))`. `sync.ts` emits a stderr warning when `parallel × workers × 2 > 16` so operators size pgbouncer / Postgres `max_connections` accordingly. **v0.41.17.0 (T2, D9):** new sibling `resolveWorkersWithClamp(engine, override, commandName, fileCount)` wrapper composes `autoConcurrency` with a per-command stderr clamp warning on PGLite. NOT a modification to shared `autoConcurrency` itself (which stays silent + used by sync/import). The wrapper is the canonical surface for every bulk-command `--workers N` flag landed in v0.41.17.0 (extract-conversation-facts, extract, edges-backfill, reindex-multimodal, reindex, reindex-code). embed.ts deliberately bypasses the wrapper and keeps `GBRAIN_EMBED_CONCURRENCY || 20` (codex #13). Per-(command, requested) stderr dedup via module-scoped warned-once set with `_resetWorkersClampWarningsForTest()` seam. Pinned by 12 cases in `test/pglite-workers-clamp.test.ts`.
- `src/core/worker-pool.ts` (v0.41.17.0 NEW, T1) — Canonical sliding-pool + bounded-semaphore primitive. Extracted from `src/commands/embed.ts` (both sliding-pool sites) and `src/commands/eval-cross-modal.ts` (`runWithLimit` semaphore). Two exports: `runSlidingPool<T>({items, workers, onItem, signal?, onError?, failureLabel?, onProgress?})` + `runWithLimit<TIn, TOut>({items, limit, fn, signal?})`. **Atomicity invariant** (`const idx = nextIdx++` is one synchronous JS statement — no `await` between read and write — guaranteed by JS single-threaded event loop) documented in module header AND enforced by `scripts/check-worker-pool-atomicity.sh` (D5) wired into `bun run verify`. Guard rejects two failure modes: importing `worker_threads` in any file that imports the helper (would cross kernel threads + break the event-loop guarantee), and inserting `await` between the `nextIdx` read and write inside the helper. **MUST_ABORT_ERROR_TAGS** set (D13) seeded with `BUDGET_EXHAUSTED` from `src/core/budget/budget-tracker.ts`; tagged errors bypass the helper's `onError` and hard-abort the pool, propagating an `AbortController.abort()` to in-flight workers' `onItem`. Budget cap becomes a structural ceiling under concurrency, not a per-caller convention. Property-tag match (`err.tag === 'BUDGET_EXHAUSTED'`) avoids cross-module import. **failures[] shape** (D7 + codex #10): `{idx, label, error}` records, NOT full items; callers supply `failureLabel(item) => string` projector. Bounded memory under 197K-page brains. Pinned by 23 cases in `test/worker-pool.test.ts` + 9 cases in `test/scripts/check-worker-pool-atomicity.test.ts` (on the CI guard itself). The shared helper drives every `--workers N` bulk command in v0.41.17.0.
- `src/commands/embed.ts` extension (v0.41.17.0, T3 REGRESSION per IRON RULE) — both inline sliding-pool sites (`embedAll` simple at `:458-467` and `embedAllStale` paginated + AbortSignal at `:586-632`) replaced with calls to `runSlidingPool` from the shared worker-pool helper. Byte-equivalent contract preserved at the invariant level (counts + cost + AbortSignal propagation + per-batch rate-limit retry firing through `embedBatchWithBackoff`); per codex #16/#17 byte-equality on progress event ORDERING is NOT promised. Existing `GBRAIN_EMBED_CONCURRENCY || 20` default preserved per codex #13 — embed bypasses the new `resolveWorkersWithClamp` wrapper because its 20-worker default pre-dates `autoConcurrency` and routing through it would silently change every existing brain's embed hot path. Pinned by 8 structural cases in `test/embed-helper-migration.test.ts` (asserts helper is wired in AND pre-migration `let nextIdx = 0` + `Promise.all(Array.from({length: numWorkers}, ...))` shapes are gone).
- `src/commands/extract-conversation-facts.ts` extension (v0.41.17.0, T5) — `--workers N` for LLM-bound fact extraction over conversation pages. Combined with the per-page advisory lock from `src/core/db-lock.ts:withRefreshingLock` (D2 + D12 — lock id `extract-conversation-facts:<source>:<slug>`, TTL `PER_PAGE_LOCK_TTL_MINUTES=2` with 20s refresh via `Math.max(15s, 120s/6)`; `LockUnavailableError` triggers D6 skip-and-continue with rate-limited log per (source, minute) + `pages_lock_skipped` counter in result + CLI exits 3 when non-zero AND no hard failures), the `deleteOrphanFactsForPage(engine, sourceId, slug)` delete-orphans-first replay safety (D11 — wipes any facts left by a prior crashed/killed run for this (sourceId, slug) before re-extracting; closes the "terminal audit row written after partial insertFacts failure" bug class codex caught in eng review), and the `assertFactsEmbeddingDimMatchesConfig(engine)` startup preflight (D15 — throws `FactsEmbeddingDimMismatchError` with paste-ready ALTER hint BEFORE the first fact insert; cached per engine via WeakMap). Result type extended with `pages_lock_skipped` + `orphan_facts_cleaned` counters. Checkpoint state migrated from per-page-mutated `cpEntries: string[]` array to shared `cpMap: Map<slug, endIso>` so JS-single-thread atomic `Map.set` survives parallel workers (codex #5/#6 fix). Minion handler `extract-conversation-facts` in `src/commands/jobs.ts` round-trips `workers` via `job.data.workers` for `--background --workers 20`. Cycle phase `cycle.conversation_facts_backfill.workers` config key (default 1; opt-in concurrency for cycle paths under brain-wide cost + walltime caps). Pinned by 17 cases in `test/extract-conversation-facts-workers.test.ts` + 27 existing extract-conversation-facts behavioral tests still green.
- `src/core/embedding-dim-check.ts` extension (v0.41.17.0, T5+T6) — facts.embedding dim drift surface. New `readFactsEmbeddingDim(engine): Promise<FactsColumnDimResult>` covers both `vector(N)` and `halfvec(N)` shapes (codex #19 — migration v40 falls back to `vector` on pgvector < 0.7). Regex ordering halfvec-before-vector pinned by tests (substring "vec" appears in "halfvec"; naive `/vector/i` would shadow). New `buildFactsAlterRecipe(dims, configured, type)` emits the paste-ready `DROP INDEX IF EXISTS idx_facts_embedding_hnsw; ALTER TABLE facts ALTER COLUMN embedding TYPE halfvec(N) USING embedding::halfvec(N); CREATE INDEX idx_facts_embedding_hnsw ON facts USING hnsw (embedding halfvec_cosine_ops) WHERE ...` flow (codex #18 — NOT bare REINDEX which doesn't rewrite the index after a column-type change). New `assertFactsEmbeddingDimMatchesConfig(engine)` is the D15 preflight — throws `FactsEmbeddingDimMismatchError` (tagged class with `tag: 'FACTS_EMBEDDING_DIM_MISMATCH'` for parity with the worker-pool's MUST_ABORT semantics) when configured dim doesn't match the column width. Result cached per-engine via `WeakMap`. PGLite engines silently skip. New doctor check `facts_embedding_width_consistency` (registered in `runDoctor` after `embedding_width_consistency`) reuses the same helpers — surfaces drift with paste-ready ALTER recipe identical to the preflight error. Pinned by 18 cases in `test/embedding-dim-check-facts.test.ts`.
- `src/core/postgres-engine.ts` extension (v0.41.17.0, T6, codex #20) — `insertFact` + `insertFacts` no longer hardcode `tx.unsafe(\`'${embedLit}'::vector\`)` for the embedding column. New `resolveFactsEmbeddingCast()` private method probes `pg_attribute` once per engine instance (cached in `_factsEmbeddingCastSuffix`) and returns `'::halfvec'` when migration v40 created the column as halfvec, else `'::vector'`. Both insert paths use the cached suffix so the cast matches the actual column type. Pre-fix all three insert sites hardcoded `::vector`; works on pgvector >= 0.7 via implicit auto-cast but fails on older pgvector. Test seam `__resetFactsEmbeddingCastCacheForTest()` clears per-engine cache.
- `src/core/cycle.ts` + `src/core/cycle/extract-atoms.ts` + `src/core/cycle/synthesize-concepts.ts` + `src/commands/extract.ts` + `src/commands/doctor.ts` + `src/core/op-checkpoint.ts` extensions (v0.41.20.0 ops-fix-wave) — six daily-driver ops pains in one bisectable wave. (1) **Batch idempotency for `extract_atoms`:** new `atomsExistingForHashes(engine, sourceId, hashes[])` exported from `src/core/cycle/extract-atoms.ts` replaces the per-hash loop that did 7K individual queries at the start of every cycle on brains with conversation-transcript corpora (5-10 min silent overhead). One batched SQL roundtrip returns the set of `content_hash16` values already extracted as atoms for this source. Fail-open: SQL error logs to stderr and returns an empty set so extraction proceeds. Powered by migration v104 `pages_atom_source_hash_idx` (partial expression index on `frontmatter->>'source_hash'` for atom rows where `deleted_at IS NULL`; Postgres uses `CREATE INDEX CONCURRENTLY` with invalid-remnant pre-drop mirroring v97 `pages_dedup_partial_index`, PGLite uses plain `CREATE INDEX`). Without this index the batch idempotency check would seq-scan pages on big brains and defeat the perf win. (2) **Shorter cycle lock TTL + active in-phase refresh:** `LOCK_TTL_MINUTES` dropped from 30 → 5 in `src/core/cycle.ts`. New exported `buildYieldDuringPhase(lock, outer)` closure calls `lock.refresh()` AND any external hook on every fire; throttled to 30s inside each phase via `maybeYield`. Fires both inside the main work loop AND immediately after every `await chat(...)` LLM call so long Haiku/Sonnet calls don't sit past TTL. `LockHandle` and `buildYieldDuringPhase` exported for test seam access. `synthesize_concepts` no longer fires `yieldDuringPhase` per-concept-group — same hook, throttled via the new shared `maybeYield` helper. A crashed cycle releases its lock 6x faster while a healthy long-running cycle keeps the lock alive. Known residual under shorter TTL: a single `await chat()` past 5 min wallclock can expire the lock mid-await without the original phase noticing — `DbLockHandle.refresh()` throwing on 0 rows affected is filed as P2 follow-up TODO-OPS-2. (3) **Progress wiring through long phases:** new `progress?: ProgressReporter` opt on `ExtractAtomsOpts` and `SynthesizeConceptsOpts`. Cycle.ts passes its phase-level reporter down (NOT a child reporter — that would produce a path collision `cycle.extract_atoms.extract_atoms.work`). Phases only call `tick()` and `heartbeat()`; cycle.ts owns `start()` and `finish()`. You see `[cycle.extract_atoms] N (atoms_created)` ticks every ~1s during both long phases instead of "start" then silence for 10+ min. (4) **`by-mention` resume:** new `mentionsFingerprint({source, type, since, gazetteerHash})` in `src/core/op-checkpoint.ts`. The gazetteer hash is the load-bearing field — adding new entity pages mid-pause shifts the hash, gets a new fingerprint, and triggers a fresh scan against the new gazetteer instead of silently skipping previously-scanned pages. `gbrain extract links --by-mention` now resumes from where it died via the existing `op_checkpoints` framework with a `flushAndCheckpoint` ordering — links flush to the DB FIRST, page keys commit to the checkpoint SECOND, persist THIRD. A crash between `batch.push()` and flush leaves the page un-checkpointed so resume re-scans it. Persist cadence: every 1000 items OR every 30s, whichever first. Clean exit clears the checkpoint. `--dry-run` deliberately skips both load and write so it stays an inspection mode. (5) **`sync_consolidation` doctor check:** multi-source brains see a paste-ready `gbrain sync --all --parallel 4 --workers 4 --skip-failed` recommendation. Single-source brains get "not applicable." SQL errors return `warn` via the check's own try/catch — outer doctor catch isn't a safe assumption. Companion "Multi-source brains" recipe block in `skills/cron-scheduler/SKILL.md` documents the `sync --all` pattern as preferred over per-source entries. (6) **Test-isolation fixes:** `test/cycle-last-full-cycle-at.test.ts` + `test/schema-cli.test.ts` migrated to per-test `GBRAIN_HOME=tempdir` isolation. Pinned by 44 new unit/PGLite cases across 9 files: `test/cycle/extract-atoms-batch.test.ts` (5 — batch idempotency), `test/cycle/cycle-lock-ttl.test.ts` (1 — regression pin on `LOCK_TTL_MINUTES === 5`), `test/op-checkpoint-mentions-fingerprint.test.ts` (7 — fingerprint sensitivity including gazetteer-hash regression guard), `test/cycle/extract-atoms-progress.test.ts` (4 — phase doesn't call start/finish, ticks fire per item), `test/cycle/synthesize-concepts-progress.test.ts` (3 — same shape), `test/cycle/yield-during-phase-refresh.test.ts` (7 — buildYieldDuringPhase actually calls lock.refresh() + outer hook, throws non-fatal), `test/cycle/yield-during-phase-throttle.test.ts` (3 — 30s throttle gate), `test/extract-by-mention-resume.test.ts` (5 — checkpoint persistence ordering, dry-run skips persist, gazetteer change invalidates, filtered pages get checkpointed), `test/doctor-sync-consolidation.test.ts` (6 — edge case matrix for source counts + archived filtering + SQL error path). Two follow-up TODOs filed in TODOS.md under "v0.41.19.0 ops-fix-wave follow-ups": `gbrain sync print-cron` subcommand (TODO-OPS-1) and lock-loss detection via `DbLockHandle.refresh()` throwing on 0 rows affected (TODO-OPS-2).
- `src/commands/sync.ts` — `gbrain sync` CLI + the `performSync` / `performFullSync` library entrypoints (consumed by the autopilot cycle and the Minion sync handler). v0.22.13 (PR #490): `performSync` wraps its body in a `gbrain-sync` writer lock so two concurrent syncs (manual + autopilot, two terminals, two Conductor workspaces) cannot both write `last_commit` and let the last writer win. Head-drift gate after the import phase re-checks `git rev-parse HEAD`; if HEAD moved (someone ran `git checkout` / `git pull` mid-sync), the bookmark refuses to advance. Vanished files now record a failedFiles entry instead of silent-skip — the silent-skip-then-advance pathology that survived prior hardening passes is dead. Worker engines wrap in try/finally so disconnect always fires (panic-path leak fix). Both PGLite-detection sites use `engine.kind === 'pglite'`. CLI accepts `--workers N` (alias `--concurrency N`), validated via `parseWorkers`. Explicit `--workers` bypasses the auto-path file-count floor; auto path defers to `autoConcurrency()`. Banner moved to stderr. **v0.34.2.0:** the inline `.sort()` over add/mod paths is replaced with `sortNewestFirst(addsAndMods)` from `src/core/sort-newest-first.ts`, so the newest-first descending-lex policy lives in one helper shared with `gbrain import` instead of drifting across two files. **v0.40.3.0 (productionized from PR #1314 by @garrytan-agents):** the load-bearing change is the lock-identity invariant — `performSync` now defaults to a per-source lock id (`gbrain-sync:<sourceId>`) whenever `opts.sourceId` is set, AND wraps the writer window in `withRefreshingLock` from `src/core/db-lock.ts` so long-running sources (the PR motivator: media-corpus / 250K+ chunks) don't lose their lock at the 30-min TTL mid-run. Legacy single-default-source brains keep the bare `tryAcquireDbLock(SYNC_LOCK_ID)` path for back-compat. `SyncOpts.lockId?: string` is the explicit override (escape hatch; production callers don't set it). The fix closes the bug class Codex's outside-voice review caught in the original PR — a `sync --all` worker on per-source lock racing against `sync --source foo` on global lock would have silently corrupted the same source. `gbrain sync --all` got a continuous worker pool: `parseWorkers`-validated `--parallel N` (default `min(sourceCount, --workers, DEFAULT_PARALLEL_SOURCES=4)` from `src/core/sync-concurrency.ts`), `parallel` long-lived async workers pulling from a shared FIFO queue (no head-of-line blocking from wave dispatch), per-source `withSourcePrefix(src.id, ...)` wrap from `src/core/console-prefix.ts` so every `slog`/`serr` line carries `[<source-id>] ` for kubectl-style greppable parallel output. `--skip-failed` and `--retry-failed` reject with a paste-ready error when combined with `--parallel > 1` (the brain-global `sync-failures.jsonl` has no per-source scope; v0.41+ TODO source-scopes it). Connection-budget stderr warning fires when `parallel × workers × 2 > 16` (the `× 2 per-file pool` factor: each per-file worker opens its own `PostgresEngine` with `poolSize=2`, so `--parallel 4 --workers 4` is actually 32 connections, not 16 — Codex caught the 2× understatement in the original plan). New exports `resolveParallelism`, `syncOneSource`, `buildSyncStatusReport`, `printSyncStatusReport`, `SyncStatusReport` back the `gbrain sources status` dashboard surface (D3 → `sources` subcommand, not a `sync` flag, so reads and writes don't share a verb). Stable `--json` envelope `{schema_version: 1, sources, parallel, ok_count, error_count}` on stdout under `--json`; human banners route to stderr via the `humanSink` helper so `jq` parses cleanly. Exit matrix: 0 = all ok, 1 = any error, 2 = cost-prompt-not-confirmed (unchanged). The dashboard SQL is the canonical `content_chunks ch JOIN pages pg ON pg.id = ch.page_id WHERE pg.deleted_at IS NULL` shape with `archived = false` filter at the caller — the original PR shipped `chunks ch JOIN ON page_slug`, which would have crashed on PGLite parse and silently zeroed on Postgres via the swallow-catch. Embedding column resolved via `resolveEmbeddingColumn(undefined, cfg)` from `src/core/search/embedding-column.ts` so Voyage / multimodal / non-default-column brains see counts against the column they actually use. Errors propagate from the dashboard SQL — no swallow-catch (Q2 sub-fix). The IRON RULE regression lives in `test/e2e/sync-status-pglite.test.ts`: real PGLite seeds 2 sources × pages × chunks, soft-deletes 1 page, archives 1 source, validates the SQL excludes both AND the active embedding column is the one used. 38 in-file `console.log`/`console.error` call sites inside `performSync*` migrated to `slog`/`serr` (top-level `runSync` orchestrator console calls intentionally stay outside the prefix scope). **v0.41.25.0 (supersedes PR #1538):** sync delete loop rewritten as interleaved per-batch resolve+delete using `engine.resolveSlugsByPaths` + `engine.deletePages` from `src/core/engine.ts`. 73K-delete commit drops from ~146K SQL round-trips (~5h on Postgres+pgbouncer) to ~292 round-trips (~2min) — closes the cascade-staleness bug class where one big-delete commit jammed every other source's sync for hours. Per-batch try-catch decomposes batch DELETE failures to per-slug `deletePage` fallback so a transient blip on batch 73 doesn't lose 500 deletes; unrecoverable per-slug failures land in `failedFiles` (matches the existing import-loop pattern). `pagesAffected` filters to D6 confirmed-deleted slugs (downstream extract/embed stop wasting work on phantoms). Same batched slug-resolve treatment for the rename loop (`gbrain sync` renames — Phase 3 in the plan; the per-file `importFile` stays per-file, only the slug-resolve N+1 gets batched). The `resolveSlugByPathOrSourcePath` single-call helper at `sync.ts:267` now delegates to `engine.resolveSlugsByPaths` when `sourceId` is set (D8 DRY — one owner of the SQL + fallback semantics), keeping legacy `executeRaw` fallback for the no-sourceId path which is functionally dead post-v0.34.1's source-resolution wiring. Legacy no-sourceId branch in the delete loop preserves correctness on a slow path; the engine batch methods require sourceId so the new fast path only fires when production threading is intact. `failedFiles` declaration hoisted to top of `performSyncInner` so both delete decompose and import loops feed the same sync-bookmark gate. **v0.41.31.0 (mode-aware cost gate):** the v0.20.0 unconditional `sync --all` ConfirmationRequired gate is superseded by a mode-aware gate driven by `willEmbedSynchronously` + `shouldBlockSync` from `src/core/embedding.ts`. federated_v2 is resolved ONCE up front (shared with the fan-out below). On the DEFERRED path (v2 on, parallel) embedding goes to per-source `embed-backfill` jobs that carry their own `$X/source/24h` cap (default $25, `SPEND_CAP_CONFIG_KEY` from `embed-backfill-submit.ts`), so the gate is INFORMATIONAL — it prints an FYI naming the backfill cap + current backlog (`sumStaleChunkChars({signature})` priced via `estimateCostFromChars` at `currentEmbeddingPricePerMTok()`) + the count of already-queued `embed-backfill` jobs (TODO-2 visibility), and NEVER exits 2. On the INLINE path (v2 off, or `--serial` without `--no-embed`) the BLOCKING gate fires only when the NEW-CONTENT estimate exceeds the `sync.cost_gate_min_usd` floor (default $0.50). The new-content estimate (`estimateInlineNewTokens`) contributes ZERO for sources provably unchanged since last sync (`isSourceUnchangedSinceSync` HEAD==last_commit + clean tree, AND `chunker_version === CURRENT`) — mirrors doctor's `sync_freshness` + sync's own do-work gate — and the full-tree ceiling for changed sources. F2 fix: the pre-existing stale backlog (NULL embeddings + signature drift) is shown informationally but NEVER gated on, because sync doesn't sweep it inline (`gbrain embed --stale` does); gating on it would block every inline cron after a model swap. New helpers `resolveCostGateFloorUsd(engine)` (reads `sync.cost_gate_min_usd`, fail-open $0.50, accepts 0) + `resolveBackfillCapUsd(engine)`. The `sync --all` SELECT widens to carry `last_commit + chunker_version` (both columns predate v0.41; no migration). JSON envelopes gain `mode` + `gate` discriminators (`dry_run | deferred_notice | below_floor | confirmation_required`). `SyncStatusReportSource` gains `backfill_queued` / `backfill_active` / `backfill_last_completed_at` (best-effort; 0/null on pre-minions brains). All embedding-cost preview math reads the configured model name via `getEmbeddingModelName()` (no hardcoded OpenAI). Pinned by `test/sync-cost-gate.serial.test.ts` + `test/sync-cost-preview.test.ts`. **v0.41.37.0 (#1569):** new `SyncOpts.noSchemaPack` (CLI `--no-schema-pack`, threaded through `performSync` AND `syncOneSource` so `sync --all` honors it) — skips `loadActivePack` entirely so no user-supplied pack page-type regex runs during import; pages fall back to legacy prefix typing. Escape hatch for completing a sync when a suspect pack regex is the suspected cause of a wedge (re-run extraction later). Same release adds a per-file BEGIN heartbeat: `if (process.env.GBRAIN_SYNC_TRACE) serr('[sync] begin import: <path>')` emitted BEFORE `importFile` (the existing `progress.tick` fires only AFTER `importFile` returns — useless when one file wedges). Off by default to avoid a line per file on huge brains; `serr` is source-prefix-aware so under `--workers >1` / `--all` the stuck file is the begin-line with no matching completion. Triage doc: `docs/architecture/serve-sync-concurrency.md` (PGLite single-writer serve↔sync contention — stop `gbrain serve` before a large PGLite sync — plus the `GBRAIN_SYNC_TRACE` + `--no-schema-pack` hang-triage recipes).
- `src/commands/import.ts` — `gbrain import` CLI + `runImport` library entrypoint. v0.34.2.0 replaces the prior positional-index checkpoint (`processedIndex: N` into a sorted file list) with a path-set checkpoint via `src/core/import-checkpoint.ts`. The walk still applies `sortNewestFirst()` for embed-cost ordering, but checkpoint correctness no longer depends on sort order. A file enters `completed: Set<relativePath>` only when its `processFile` returns success (including content-hash short-circuit no-ops); failed files never enter the set, so the next run retries them automatically with no manual `~/.gbrain/import-checkpoint.json` delete. Three bug classes died: parallel-import-with-slow-worker drops the slow file on crash-resume (closed — the slow file isn't in `completed` until its own `processFile` resolves), failed-file-bumps-counter-past-itself (closed — failures don't add to `completed`), and v0.33.x sort-flip-drops-newest-N-on-cross-version-resume (closed — order is no longer part of the checkpoint). Old positional checkpoints are detected and discarded with a stderr line on first resume; re-walking is cheap because `content_hash` short-circuits unchanged files. Checkpoint persists every 100 successful adds, not every 100 processed files, so a long failure tail doesn't churn the JSON. Pinned by `test/import-checkpoint.test.ts` (18 unit cases over the helpers) + `test/import-resume.test.ts` (5 integration cases under PGLite, including the SLUG_MISMATCH retry regression codex caught during plan-eng-review).
- `src/core/import-checkpoint.ts` (v0.34.2.0) — `loadCheckpoint(brainDir)`, `saveCheckpoint(brainDir, completed)`, `resumeFilter(files, completed, brainDir)`, `clearCheckpoint()`, plus the `ImportCheckpoint` type. Path-set checkpoint format (`{schema_version, brainDir, completed: string[]}`) replaces the v0.33.x positional `{processedIndex: N}` format. Atomic write via `.tmp` + `rename()` so a mid-write crash never leaves a partial JSON. `loadCheckpoint` returns `null` on: missing file, malformed JSON, brainDir mismatch (you ran import against a different brain), and the old positional format (logged to stderr before being discarded). `resumeFilter` returns `{toProcess, skippedCount}` — pure, no I/O, deterministic. `clearCheckpoint` is no-op-on-missing for clean-exit cleanup. Honors `GBRAIN_HOME` via `gbrainPath()` so test isolation via `withEnv({GBRAIN_HOME: tmpdir})` works without monkey-patching the fs layer. Best-effort persistence — `saveCheckpoint` logs warnings on write errors but never throws, so import keeps making progress even if disk is full.
- `src/core/sort-newest-first.ts` (v0.34.2.0) — single source of truth for the descending-lex sort that `gbrain import` and `gbrain sync` both apply. Mutates in place (Array.prototype.sort semantics), returns the same array reference for fluent chaining. Empty/single-element inputs short-circuit. Future ordering changes flip one line in this helper instead of touching two CLI commands. Pinned by `test/sort-newest-first.test.ts` (5 hermetic cases: descending order, mixed prefixes, empty input, single-element input, in-place-mutation contract).
- `src/core/cycle.ts` — v0.17 brain maintenance cycle primitive (extended to **9 phases in v0.29**). `runCycle(engine: BrainEngine | null, opts: CycleOpts): Promise<CycleReport>` composes phases in semantically-driven order: **lint → backlinks → sync → synthesize → extract → patterns → recompute_emotional_weight → embed → orphans**. v0.29 adds the `recompute_emotional_weight` phase between patterns and embed; it sees the union of `syncPagesAffected` + `synthesizeWrittenSlugs` for incremental mode, or all pages when neither anchor is set (full backfill via `gbrain dream --phase recompute_emotional_weight`). v0.29 also extends `CycleReport.totals` with `pages_emotional_weight_recomputed` (additive, schema_version stays "1"). v0.23's `synthesize` phase runs after sync (cross-references see fresh brain) and before extract (auto-link materializes its writes); `patterns` runs after extract so it reads a fresh graph (codex finding #7 — subagent put_page sets `ctx.remote=true` and skips auto-link/timeline by default; extract is the canonical materialization). Three callers: `gbrain dream` CLI, `gbrain autopilot` daemon's inline path, and the Minions `autopilot-cycle` handler. Coordination via `gbrain_cycle_locks` DB table + `~/.gbrain/cycle.lock` file lock with PID-liveness for PGLite. `CycleReport.schema_version: "1"` is stable; totals additively grew in v0.23 (`transcripts_processed`, `synth_pages_written`, `patterns_written`). `yieldBetweenPhases` runs between phases. **v0.23 added `yieldDuringPhase`** for in-phase keepalive — synthesize/patterns call it during long waits to renew the cycle-lock TTL. Engine nullable; lock-skip on read-only phase selections. v0.22.1 (#403): `CycleOpts.signal?: AbortSignal` propagates the worker's abort signal; `checkAborted()` fires between every phase. v0.22.1 (#417): `runPhaseSync` returns `pagesAffected` via `SyncPhaseResult`; `runCycle` captures it and threads to `runPhaseExtract` as the 4th arg. v0.22.1 (Codex F2): `runPhaseSync` takes `willRunExtractPhase: boolean` and sets `noExtract: phases.includes('extract')` so `gbrain dream --phase sync` doesn't silently lose extraction. v0.22.5 (#475): `resolveSourceForDir(engine, brainDir)` threads `sourceId` to `performSync()` so sync reads the per-source `sources.last_commit` anchor instead of the drift-prone global `config.sync.last_commit` key.
- `src/core/cycle/synthesize.ts` (v0.23) — Synthesize phase: conversation-transcript-to-brain pipeline. Reads from `dream.synthesize.session_corpus_dir`, runs cheap Haiku verdict (cached in `dream_verdicts`), then fans out one Sonnet subagent per worth-processing transcript with `allowed_slug_prefixes` (sourced from `skills/_brain-filing-rules.json` `dream_synthesize_paths.globs`). Orchestrator collects slugs from `subagent_tool_executions` (NOT `pages.updated_at` — codex finding #2) and reverse-renders DB → markdown via `serializeMarkdown`. Cooldown via `dream.synthesize.last_completion_ts`, written ONLY on success. Idempotency key `dream:synth:<file_path>:<content_hash>`. Auto-commit deferred to v1.1 (codex #5). `--dry-run` runs Haiku, skips Sonnet (codex #8). Subagent never gets fs-write access. **v0.23.2:** `renderPageToMarkdown` (now exported) stamps `dream_generated: true` and `dream_cycle_date` into every reverse-write's frontmatter; `writeSummaryPage` does the same on the dream-cycle summary index. The marker is the explicit identity surface checked by `isDreamOutput` in `transcript-discovery.ts` — replaces the v0.23.1 content-prefix heuristic that could miss real output (`serializeMarkdown` doesn't embed slugs in body) and false-positive on user transcripts citing brain pages. `judgeSignificance` and `JudgeClient` are exported; `judgeSignificance` accepts a `verdictModel` parameter (default `claude-haiku-4-5-20251001`) loaded from `dream.synthesize.verdict_model` via `loadSynthConfig`. **v0.30.2:** model-aware chunker `splitTranscriptByBudget(content, contentHash, maxChars)` splits oversized transcripts at paragraph boundaries (`## Topic:` → `---` → `\n` ladder) using a deterministic offset seeded from the first 32 bits of `contentHash` so retries chunk identically. Per-chunk char budget computed from `MODEL_CONTEXT_TOKENS[resolvedModel] × 0.9 × 3.5 chars/token`; non-Anthropic ids fall back to a 180K-token safe default with a once-per-process stderr warning. Operator overrides: `dream.synthesize.max_prompt_tokens` (floor 100K, wins when set) and `dream.synthesize.max_chunks_per_transcript` (default 24). Per-chunk idempotency keys `dream:synth:<filePath>:<hash16>:c<i>of<n>`; single-chunk transcripts preserve the legacy `dream:synth:<filePath>:<hash16>` key byte-for-byte (D8 lookup), so existing brains skip with `already_synthesized_legacy_single_chunk` instead of re-spending Sonnet on upgrade. `collectChildPutPageSlugs` raw-fetches every (job_id, slug) pair (not `SELECT DISTINCT`) and rewrites bare-hash6 slugs to `<hash6>-c<idx>` for chunked children (D6 — orchestrator-side, zero Sonnet trust). Cap-hit skips don't write to `dream_verdicts`, so raising the cap on next run re-attempts cleanly. D7 scope: bounds INITIAL prompt size only; tool-loop turn-N accumulation is caught by the v0.30.2 terminal-error classification in `subagent.ts`, not bounded ahead of time. **v0.41+ community-PR-wave (reworked PR #1349):** `makeHaikuClient()` replaced by gateway-routed `makeJudgeClient(verdictModel)` exported helper — mirrors `tryBuildGatewayClient` in `src/core/think/index.ts:579-637` (the v0.35.5.0 #952 pattern). Construction-time provider/key probe returns `null` on a clear miss (unknown provider id via `resolveRecipe` AIConfigError, or Anthropic provider with no key via `hasAnthropicKey()` matching the same env + config-file pattern think uses). Verdict loop wraps `judgeSignificance` in try/catch for `AIConfigError` so mid-run provider failures (revoked key, recipe misconfig) surface as per-transcript `worth=false, reasons=['gateway error: ...']` instead of crashing the phase. Canonical config key `models.dream.synthesize_verdict` (per `PER_TASK_KEYS` in `src/core/model-config.ts`); contributor's parallel `DEEPSEEK_API_KEY` fetch adapter dropped in favor of recipe-registered providers (DeepSeek, OpenRouter, Voyage, Ollama, llama-server, ...). `JudgeClient` interface signature preserved verbatim for test-seam stability. CI guard at `scripts/check-gateway-routed-no-direct-anthropic.sh` prevents future contributors from re-introducing `new Anthropic()` here or in `think/index.ts`. Pinned by 13 cases in `test/cycle/synthesize-gateway-adapter.test.ts` (A1-A9 unit + R3 parsed-verdict semantic parity + R3 corollary) and 1 E2E case in `test/e2e/dream-synthesize-pglite.test.ts` ('gateway-adapter mid-run AIConfigError catch') plus 4 R1-R4 critical regression pins in `test/cycle/regression-pr-wave-r1-r2-r4.test.ts`. **v0.41.5.0:** narrow `anthropic:` prefix fix at the queue.add boundary (lines 395-404). `resolveModel` returns bare ids from `TIER_DEFAULTS`/`DEFAULT_ALIASES` (e.g. `claude-sonnet-4-6`); the subagent validator requires `provider:model` form and was rejecting with `unknown provider`, dropping synthesize to `status: fail` with `SYNTH_PHASE_FAIL`. Conditional prefix at the call site (only when no colon AND starts with `claude-`) avoids changing the shared constants which would ripple across every `resolveModel` caller.
- `scripts/check-gateway-routed-no-direct-anthropic.sh` (v0.41+ community-PR-wave) — CI guard that fails the build if `src/core/cycle/synthesize.ts` or `src/core/think/index.ts` reintroduces a runtime `new Anthropic()` constructor call or a value-shaped `import Anthropic from '@anthropic-ai/sdk'` import. Type-only imports (`import type Anthropic from '@anthropic-ai/sdk'`) stay allowed for adapter types. Comment lines (`//` or ` *` prefixes) are excluded so historical JSDoc references don't false-fire. Mirrors `scripts/check-jsonb-pattern.sh`. Wired into `bun run verify` and `bun run check:all`. Extend `GUARDED_FILES` in the script when migrating another file off direct SDK construction.
- `src/core/cycle/patterns.ts` (v0.23) — Patterns phase: cross-session theme detection over reflections within `dream.patterns.lookback_days` (default 30). Names a pattern only when ≥`dream.patterns.min_evidence` (default 3) reflections support it. Single Sonnet subagent; same allow-list path as synthesize. Runs AFTER `extract` so the graph is fresh.
- `src/core/cycle/extract-facts.ts` (v0.32.2, extended v0.35.6.0) — extract_facts cycle phase. v0.32.2 contract: fence is canonical; per-page wipe (`deleteFactsForPage`) + reinsert from `parseFactsFence` + `extractFactsFromFenceText` + `engine.insertFacts`. Empty-fence guard refuses when v0.31 legacy rows (`row_num IS NULL AND entity_slug IS NOT NULL`) pend the v0_32_2 backfill (status: warn, hint: `gbrain apply-migrations --yes`). **v0.35.6.0** adds a phantom-redirect pre-pass that runs AFTER the legacy-row guard, BEFORE the main reconcile loop. When `opts.brainDir` is set, `runPhantomRedirectPass(engine, brainDir, sourceId, dryRun)` walks unprefixed-slug pages capped by `GBRAIN_PHANTOM_REDIRECT_LIMIT` (default 50). The pass returns `touched_canonicals` — canonical slugs whose disk fence was merged with phantom rows; `runExtractFacts` UNIONs them into the main reconcile slug set so canonical's DB facts derive from the merged fence in the same cycle (round-14 scenario-B fix: phantom had only-on-disk fence, no DB facts). `ExtractFactsResult` gains six phantom fields: `phantomsScanned`, `phantomsRedirected`, `phantomsAmbiguous`, `phantomsSkippedDrift`, `phantomsLockBusy`, `phantomsMorePending`. Three of those bubble to `CycleReport.totals` (`phantoms_redirected`, `phantoms_ambiguous`, `phantoms_skipped_drift`).
- `src/core/entities/resolve.ts` (v0.30+, extended v0.35.6.0) — Free-form entity name → canonical slug resolution. `resolveEntitySlug(engine, source_id, raw)`: exact slug → fuzzy (pg_trgm @ 0.4 threshold) → bare-name prefix expansion (`people/<token>-%` then `companies/<token>-%` using correlated-subquery `connection_count` for tiebreaker) → deterministic `slugify` fallback. **v0.35.6.0** exports two new helpers for the phantom-redirect pass: `resolvePhantomCanonical(engine, sourceId, phantomSlug)` — variant that SKIPS the exact-slug step (codex #1: phantom slug `'alice'` exact-matches itself, would make the redirect handler a no-op); returns the canonical only when result is non-null AND contains `/`. `findPrefixCandidates(engine, sourceId, token)` — standalone SQL query returning ALL candidates across `PREFIX_EXPANSION_DIRS` (currently hardcoded `['people', 'companies']`) using `slug LIKE ANY($N::text[])` over patterns `dir/token` + `dir/token-%`; cap of 10 ordered by `connection_count DESC, slug ASC`. NOT a wrapper around `tryPrefixExpansion` because that path returns per-dir top-1 and suppresses ambiguity by design (codex #11). Pinned by `test/phantom-redirect.test.ts` resolvePhantomCanonical describe (3 cases) + findPrefixCandidates describe (6 cases including multi-dir ambiguity and the `people/aliceberg`-doesn't-match-`alice` false-positive guard).
- `src/core/cycle/phantom-redirect.ts` (v0.35.6.0) — Phantom-redirect orchestrator. Exports `runPhantomRedirectPass(engine, brainDir, sourceId, dryRun): Promise<PhantomPassResult>` (the per-cycle wrapper that acquires `gbrain-sync` writer lock once for the entire pass, 30s bounded retry, walks up-to-`GBRAIN_PHANTOM_REDIRECT_LIMIT` unprefixed phantoms) + `tryRedirectPhantom(engine, page, sourceId, brainDir, dryRun): Promise<RedirectResult>` (single-phantom orchestrator) + `stripFenceAndFrontmatterAndLeadingH1` (pure helper for the body-shape gate — strips facts fence including the preceding `## Facts` heading and the leading H1; zero residue = phantom). Handler order: body-shape gate → `resolvePhantomCanonical` (codex #1: bypasses exact-self-match) → `findPrefixCandidates` ambiguity check (codex #11: standalone query, not per-dir top-1) → `fenceDbDrift` bi-directional check (rounds 27/29/30) → dry-run early exit → materialize canonical via `serializeMarkdown` if DB-only (codex #6) → append phantom fence rows to canonical's disk fence with `(claim, valid_from)` dedup-guard + row_num continuation → `engine.refreshPageBody` with SHA-256 content_hash recomputed via the import-file shape (codex #7) → `engine.migrateFactsToCanonical` (codex #3/#4/#12 lossless preservation) → `engine.rewriteLinks` (DB FK rewrite; wiki-link text rewrite is a documented follow-up per codex #5) → `engine.softDeletePage` + `engine.deleteFactsForPage(phantom)` + `fs.unlinkSync(phantomPath)` (rounds 19/20). `RedirectResult.canonical` populated on outcome `'redirected'` (incl. dry-run preview) so the caller can populate `touched_canonicals`. Idempotent on re-run: phantom soft-deleted → predicate fails (`deleted_at IS NULL` filter); migrate UPDATE matches no rows; dedup-guard prevents double-append.
- `src/core/facts/phantom-audit.ts` (v0.35.6.0) — JSONL audit at `${resolveAuditDir()}/phantoms-YYYY-Www.jsonl`. Pattern copy of `src/core/audit-slug-fallback.ts` (ISO-week rotation, honors `GBRAIN_AUDIT_DIR`). Exports `logPhantomEvent(record)` + `readRecentPhantomEvents(days)` + `computePhantomAuditFilename(now?)`. Records every outcome: `redirected | ambiguous | drift | no_canonical | not_phantom_has_residue | pass_skipped_lock_busy`. Best-effort writes — stderr warn on failure, never throws. Separate file from `stub-guard-audit.ts` because the consumer + lifecycle are distinct (stub-guard logs PREVENTIVE blocks; phantom-audit logs CLEANUP decisions, will be read by a future T9 doctor `phantoms_pending` check).
- `src/core/cycle/emotional-weight.ts` (v0.29) — Pure function `computeEmotionalWeight({tags, takes}, {highEmotionTags?, userHolder?})`. Deterministic 0..1 score: tag-emotion boost (max 0.5, case-insensitive match against `HIGH_EMOTION_TAGS` seed list), take density (0.1/take, capped at 0.3), take avg weight (0..0.1), user-holder ratio (0..0.1 over active takes; default holder = 'garry'). Total clamped to [0..1]. Anglocentric / personal-life-biased seed list intentional; users override via config key `emotional_weight.high_tags` (JSON array). `userHolder` overridable via `emotional_weight.user_holder`.
- `src/core/cycle/anomaly.ts` (v0.29) — Pure stats helpers for `find_anomalies`. `meanStddev` returns sample stddev (n-1 denominator) and (0,0) for empty input. `computeAnomaliesFromBuckets(baseline, today, sigma, limit)` takes densified daily-count buckets + today's counts per cohort, returns `AnomalyResult[]`. Zero-stddev fallback: cohort fires when `count > mean + 1`, with `sigma_observed = count - mean` as a finite sort proxy (no NaN). Brand-new cohorts (no baseline) have `mean=0, stddev=0` so the fallback fires at count >= 2. Sorted by `sigma_observed` desc, top `limit` (default 20). `page_slugs` capped at 50 per cohort.
- `src/core/cycle/recompute-emotional-weight.ts` (v0.29) — Cycle phase orchestrator. Two SQL round-trips total: `engine.batchLoadEmotionalInputs(slugs?)` → `computeEmotionalWeight` (per-row pure function) → `engine.setEmotionalWeightBatch(rows)`. Reads config keys `emotional_weight.high_tags` (JSON array, falls back to default seed list on parse error) and `emotional_weight.user_holder`. Empty `affectedSlugs` array short-circuits with zero-work success. dry-run mode reports the would-write count without touching the DB. Engine throw bubbles into `status: 'fail'` with code `RECOMPUTE_EMOTIONAL_WEIGHT_FAIL` so the cycle continues.
- `src/core/transcripts.ts` (v0.29) — `listRecentTranscripts(engine, opts)` library reused by both the `gbrain transcripts recent` CLI and the `get_recent_transcripts` MCP op. Reads `dream.synthesize.session_corpus_dir` + `dream.synthesize.meeting_transcripts_dir` config keys (same as `discoverTranscripts`); walks for `.txt` files within `days`; applies `isDreamOutput` guard from `transcript-discovery.ts` (skips dream-generated files); returns `{path, date, mtime, length, summary}[]` sorted newest-first. Summary mode (default true) returns first non-empty line + ~250 trailing chars. Full mode caps at 100KB/file. Missing/non-existent corpus dirs return `[]`, not error. **Trust gate lives in the op handler, not here**: the op throws `permission_denied` for `ctx.remote === true`; this library is a trusted library function used by both the gated op and the local CLI.
- `src/core/operations-descriptions.ts` (v0.29) — Constants module for tool descriptions. Pinned via `test/operations-descriptions.test.ts`. Houses `GET_RECENT_SALIENCE_DESCRIPTION`, `FIND_ANOMALIES_DESCRIPTION`, `GET_RECENT_TRANSCRIPTS_DESCRIPTION` plus the redirect-edited `LIST_PAGES_DESCRIPTION`, `QUERY_DESCRIPTION`, `SEARCH_DESCRIPTION`. Stable surface for the Tier-2 LLM routing eval — extracting them keeps the test from binding to whatever was in `operations.ts` at test-run time.
- `src/core/cycle/transcript-discovery.ts` (v0.23) — Pure filesystem walk for synthesize. `discoverTranscripts(opts)` filters `.txt` files by date range, min_chars, and word-boundary regex `excludePatterns` (Q-3: `medical` matches "medical advice" but NOT "comedical"; power users may pass full regex). `readSingleTranscript(path)` is the `gbrain dream --input <file>` ad-hoc path. **v0.23.2 self-consumption guard:** `DREAM_OUTPUT_MARKER_RE` (anchored at frontmatter open `---\n`, optional BOM + CRLF tolerance, scans first 2000 chars for `dream_generated: true` with case-insensitive value and word boundary on `true`) drives `isDreamOutput(content, bypass=false)`. Both `discoverTranscripts` and `readSingleTranscript` skip matching files and emit a `[dream] skipped <basename>: dream_generated marker` stderr log (no more silent skips). `bypassGuard?: boolean` on `DiscoverOpts` and `readSingleTranscript`'s opts disables the guard for the explicit `--unsafe-bypass-dream-guard` escape hatch only — never auto-applied for `--input`. Replaces v0.23.1's `DREAM_OUTPUT_SLUGS` content-prefix list.
- `src/commands/dream.ts` — v0.17 `gbrain dream` CLI; ~80-line thin alias over `runCycle`. brainDir resolution requires explicit `--dir` OR `sync.repo_path` config. Flags: `--dry-run`, `--json`, `--phase <name>`, `--pull`, `--dir <path>`. **v0.23 added** `--input <file>` (ad-hoc transcript, implies `--phase synthesize`), `--date YYYY-MM-DD`, `--from <d> --to <d>` (backfill range). Conflict detection: `--input` + `--date` exits 2. ISO date validation. `--dry-run` runs Haiku significance verdict but skips Sonnet synthesis (codex finding #8 — NOT zero LLM calls). Exit code 1 on status=failed. **v0.23.2 added** `--unsafe-bypass-dream-guard` (long-form intentional, plumbed through `runCycle.synthBypassDreamGuard` → `SynthesizePhaseOpts.bypassDreamGuard` → `discoverTranscripts({bypassGuard})` and `readSingleTranscript({bypassGuard})`). Loud stderr warning fires at synthesize-phase entry when set. Never auto-applied for `--input` so any caller can't silently re-trigger the loop bug.
- `src/commands/friction.ts` + `src/core/friction.ts` (v0.23) — `gbrain friction {log,render,list,summary}` reporter. Append-only JSONL under `$GBRAIN_HOME/friction/<run-id>.jsonl`. Schema is a flat extension of `StructuredAgentError` (D20). Render groups by severity → phase, defaults to `--redact` for md output (strips `$HOME`/`$CWD` to placeholders so reports paste safely in PRs). Run-id resolves from `--run-id` > `$GBRAIN_FRICTION_RUN_ID` > `standalone.jsonl`. Skills the claw-test exercises gain a `_friction-protocol.md` callout so agents know when to log friction.
- `src/commands/claw-test.ts` + `src/core/claw-test/` (v0.23) — `gbrain claw-test [--scenario <name>] [--live --agent openclaw]`. End-to-end "fresh user" friction harness. Two modes: scripted (CI gate, agent-free) and live (real openclaw subprocess, $1–2 in tokens). Sets `GBRAIN_HOME=<tempdir>` for hermeticity and captures gbrain's `--progress-json` events from each child's stderr to verify expected phases ran (`import.files`, `extract.links_fs`, `doctor.db_checks`). Phases for scripted mode: setup → install_brain (`gbrain init --pglite`) → import (`--no-embed`) → query → extract → verify (`gbrain doctor --json`, asserts `status: 'ok'`) → render. Live mode hands `BRIEF.md` from `test/fixtures/claw-test-scenarios/<name>/` to the agent runner. v1 ships with the OpenClaw runner only (`src/core/claw-test/runners/openclaw.ts`, invokes `openclaw agent --local --agent <name> --message <brief>`); hermes runner deferred to v1.1. Transcript capture (`transcript-capture.ts`) uses `fs.createWriteStream` with `'drain'`-event backpressure — D17 fix for the 256KB-burst child-stall scenario. v0.18 upgrade scenario seeded via `seed-pglite.ts` SQL replay.
- `skills/_friction-protocol.md` (v0.23) — shared cross-cutting convention skill (like `_brain-filing-rules.md`). Tells agents when to call `gbrain friction log` and how to choose a severity. Routes to friction CLI from any skill the claw-test exercises.
- `scripts/check-progress-to-stdout.sh` — CI guard against regressing to `\r`-on-stdout progress. Wired into `bun run test` via `scripts/check-progress-to-stdout.sh && bun test` in package.json.
- `docs/progress-events.md` — Canonical JSON event schema reference. Stable from v0.15.2, additive only.
- `src/core/markdown.ts` — Frontmatter parsing + body splitter. `splitBody` requires an explicit timeline sentinel (`<!-- timeline -->`, `--- timeline ---`, or `---` immediately before `## Timeline`/`## History`). Plain `---` in body text is a markdown horizontal rule, not a separator. `inferType` auto-types `/wiki/analysis/` → analysis, `/wiki/guides/` → guide, `/wiki/hardware/` → hardware, `/wiki/architecture/` → architecture, `/writing/` → writing (plus the existing people/companies/deals/etc heuristics).
- `scripts/check-jsonb-pattern.sh` — CI grep guard. Fails the build if anyone reintroduces (a) the `${JSON.stringify(x)}::jsonb` interpolation pattern (postgres.js v3 double-encodes it), or (b) `max_stalled INTEGER NOT NULL DEFAULT 1` in any schema source file (v0.15.1 #219 regression guard — must be DEFAULT 5 to preserve SIGKILL-rescue). Wired into `bun test`.
- `scripts/check-source-id-projection.sh` (v0.32.8, PR #860) — CI grep guard for the multi-source bug class. Greps `src/core/postgres-engine.ts` + `src/core/pglite-engine.ts` for `SELECT.*FROM pages` projections matching the `rowToPage` feeder shape (id + slug + type + title) and fails if `source_id` is missing. After v0.32.8 `Page.source_id` is required at the type level; a projection that drops the column produces `Page` rows with `source_id: undefined` while TypeScript's `: string` lies about it. Codex's outside-voice review caught two pre-existing projections (`getPage`, `putPage RETURNING`) that lacked the column. Wired into `bun run verify` + `bun run check:all`.
- `docker-compose.ci.yml` + `scripts/ci-local.sh` (v0.23.1) — Local CI gate. `bun run ci:local` spins up `pgvector/pgvector:pg16` + `oven/bun:1` with named volumes (`gbrain-ci-pg-data`, `gbrain-ci-node-modules`, `gbrain-ci-bun-cache`), runs gitleaks on host, smoke-tests `scripts/run-e2e.sh` argv handling, runs unit tests with `DATABASE_URL` unset (matches GH Actions structure), then runs all 29 E2E files sequentially. `--diff` swaps in the diff-aware selector; `--no-pull` skips upstream pulls; `--clean` nukes named volumes. Postgres host port defaults to 5434 (avoids 5432 manual `gbrain-test-pg` and 5433 sibling-project conflict); override with `GBRAIN_CI_PG_PORT=NNNN`. Stronger gate than current PR CI's 2-file Tier 1 set — closes the "push-and-wait" feedback loop pre-push.
- `scripts/select-e2e.ts` + `scripts/e2e-test-map.ts` (v0.23.1) — Diff-aware E2E test selector. Reads three git sources (committed `origin/master...HEAD`, working-tree `HEAD`, and `git ls-files --others --exclude-standard` for untracked, NOT-gitignored files), classifies as EMPTY / DOC_ONLY / SRC. Fail-closed by design: EMPTY → all 29 files (clean branch shouldn't run nothing), DOC_ONLY (every path matches the README/CLAUDE/AGENTS/CHANGELOG/TODOS allowlist) → empty stdout, SRC → escape-hatch paths (schema, package.json, skills/) trigger all; otherwise the hand-tuned `E2E_TEST_MAP` glob → tests narrows; an unmapped src/ change still emits ALL files, never silently nothing. Pure-function exports (`selectTests`, `classify`, `matchGlob`) so it's trivial to test and fork. `bun run ci:select-e2e` prints the current selection on stdout, pipe-friendly. `test/select-e2e.test.ts` covers all 4 branches plus 3 codex regression guards (skills/, untracked files, unmapped src/) — 24 cases.
- `scripts/run-e2e.sh` (v0.23.1 update) — Sequential E2E runner. Now accepts an optional argv-driven file list (used by `ci:local:diff` to pipe in selector output) and a `--dry-run-list` flag that prints the resolved file list and exits (used by `ci-local.sh`'s startup smoke-test). Falls back to `test/e2e/*.test.ts` when invoked with no args.
- `scripts/llms-config.ts` + `scripts/build-llms.ts` — Generator for `llms.txt` (llmstxt.org-spec web index) + `llms-full.txt` (inlined single-fetch bundle). Curated config drives both. Run `bun run build:llms` after adding a new doc. `LLMS_REPO_BASE` env var lets forks regenerate with their own URL base. `FULL_SIZE_BUDGET` (600KB) caps the inline bundle; generator WARNs if exceeded. Committed output is not analogous to `schema-embedded.ts` (no runtime consumer); we commit for GitHub browsing and fork-safe fetching.
- `AGENTS.md` — Local-clone entry point for non-Claude agents (Codex, Cursor, OpenClaw, Aider). Mirrors `CLAUDE.md` intent via relative links. Claude Code keeps using `CLAUDE.md`.
- `docs/UPGRADING_DOWNSTREAM_AGENTS.md` — Patches for downstream agent skill forks to apply when upgrading. Each release appends a new section. v0.10.3 includes diffs for brain-ops, meeting-ingestion, signal-detector, enrich.
- `src/core/schema-embedded.ts` — AUTO-GENERATED from schema.sql (run `bun run build:schema`)
- `src/schema.sql` — Full Postgres + pgvector DDL (source of truth, generates schema-embedded.ts)
- `src/commands/integrations.ts` — Standalone integration recipe management (no DB needed). Exports `getRecipeDirs()` (trust-tagged recipe sources), SSRF helpers (`isInternalUrl`, `parseOctet`, `hostnameToOctets`, `isPrivateIpv4`). Only package-bundled recipes are `embedded=true`; `$GBRAIN_RECIPES_DIR` and cwd `./recipes/` are untrusted and cannot run `command`/`http`/string health checks.
- `src/core/search/expansion.ts` — Multi-query expansion via Haiku. Exports `sanitizeQueryForPrompt` + `sanitizeExpansionOutput` (prompt-injection defense-in-depth). Sanitized query is only used for the LLM channel; original query still drives search.
- `recipes/` — Integration recipe files (YAML frontmatter + markdown setup instructions)
- `docs/guides/` — Individual SKILLPACK guides (broken out from monolith)
- `docs/integrations/` — "Getting Data In" guides and integration docs
- `docs/architecture/infra-layer.md` — Shared infrastructure documentation
- `docs/ethos/THIN_HARNESS_FAT_SKILLS.md` — Architecture philosophy essay
- `docs/ethos/MARKDOWN_SKILLS_AS_RECIPES.md` — "Homebrew for Personal AI" essay
- `docs/guides/repo-architecture.md` — Two-repo pattern (agent vs brain)
- `docs/guides/sub-agent-routing.md` — Model routing table for sub-agents
- `docs/guides/skill-development.md` — 5-step skill development cycle + MECE
- `docs/guides/idea-capture.md` — Originality distribution, depth test, cross-linking
- `docs/guides/quiet-hours.md` — Notification hold + timezone-aware delivery
- `docs/guides/diligence-ingestion.md` — Data room to brain pages pipeline
- `docs/designs/HOMEBREW_FOR_PERSONAL_AI.md` — 10-star vision for integration system
- `docs/mcp/` — Per-client setup guides (Claude Desktop, Code, Cowork, Perplexity)
- BrainBench (benchmark suite + corpus): lives in the separate [gbrain-evals](https://github.com/garrytan/gbrain-evals) repo. Not installed alongside gbrain.
- `skills/_brain-filing-rules.md` — Cross-cutting brain filing rules (referenced by all brain-writing skills)
- `skills/RESOLVER.md` — Skill routing table (based on the agent-fork AGENTS.md pattern)
- `skills/conventions/` — Cross-cutting rules (quality, brain-first, model-routing, test-before-bulk, cross-modal)
- `skills/_output-rules.md` — Output quality standards (deterministic links, no slop, exact phrasing)
- `skills/signal-detector/SKILL.md` — Always-on idea+entity capture on every message
- `skills/brain-ops/SKILL.md` — Brain-first lookup, read-enrich-write loop, source attribution
- `skills/idea-ingest/SKILL.md` — Links/articles/tweets with author people page mandatory
- `skills/media-ingest/SKILL.md` — Video/audio/PDF/book with entity extraction
- `skills/meeting-ingestion/SKILL.md` — Transcripts with attendee enrichment chaining
- `skills/citation-fixer/SKILL.md` — Citation format auditing and fixing
- `skills/repo-architecture/SKILL.md` — Filing rules by primary subject
- `skills/skill-creator/SKILL.md` — Create conforming skills with MECE check
- `skills/daily-task-manager/SKILL.md` — Task lifecycle with priority levels
- `skills/daily-task-prep/SKILL.md` — Morning prep with calendar context
- `skills/cross-modal-review/SKILL.md` — Quality gate via second model
- `skills/cron-scheduler/SKILL.md` — Schedule staggering, quiet hours, idempotency
- `skills/reports/SKILL.md` — Timestamped reports with keyword routing
- `skills/testing/SKILL.md` — Skill validation framework
- `skills/soul-audit/SKILL.md` — 6-phase interview for SOUL.md, USER.md, ACCESS_POLICY.md, HEARTBEAT.md
- `skills/webhook-transforms/SKILL.md` — External events to brain signals
- `skills/data-research/SKILL.md` — Structured data research: email-to-tracker pipeline with parameterized YAML recipes
- `skills/minion-orchestrator/SKILL.md` — Unified background-work skill (v0.20.4 consolidation of the former `minion-orchestrator` + `gbrain-jobs` split). Two lanes: shell jobs via `gbrain jobs submit shell --params '{"cmd":"..."}'` (operator/CLI only; MCP throws `permission_denied` for protected names) and LLM subagents via `gbrain agent run` (user-facing entrypoint). Shared Preconditions block, parent-child DAGs with depth/cap/timeouts, `child_done` inbox for fan-in, PGLite `--follow` inline path for dev. Triggers narrowed from bare `"gbrain jobs"` to `"gbrain jobs submit"` + `"submit a gbrain job"` so `stats`/`prune`/`retry` questions fall through to `gbrain --help`.
- `templates/` — SOUL.md, USER.md, ACCESS_POLICY.md, HEARTBEAT.md templates
- `skills/migrations/` — Version migration files with feature_pitch YAML frontmatter
- `src/commands/publish.ts` — Deterministic brain page publisher (code+skill pair, zero LLM calls)
- `src/commands/backlinks.ts` — Back-link checker and fixer (enforces Iron Law)
- `src/commands/lint.ts` — Page quality linter (catches LLM artifacts, placeholder dates)
- `src/commands/report.ts` — Structured report saver (audit trail for maintenance/enrichment)
- `src/core/destructive-guard.ts` (v0.26.5) — three-layer protection against accidental data loss in gbrain. `assessDestructiveImpact(engine, sourceId)` counts pages/chunks/embeddings/files for a source. `checkDestructiveConfirmation(impact, opts)` is the fail-closed gate (`--confirm-destructive` required when data is present; `--yes` alone is rejected). `softDeleteSource` / `restoreSource` / `listArchivedSources` / `purgeExpiredSources` drive the source-level archive lifecycle via the column shape introduced in migration v34 (`sources.archived BOOLEAN`, `archived_at TIMESTAMPTZ`, `archive_expires_at TIMESTAMPTZ`). v0.26.5 added the page-level analog through `BrainEngine.softDeletePage` / `restorePage` / `purgeDeletedPages` plus `pages.deleted_at TIMESTAMPTZ` and a partial purge index. The MCP `delete_page` op rewires to `softDeletePage`; new ops `restore_page` (`scope: write`) and `purge_deleted_pages` (`scope: admin`, `localOnly: true`) round out the surface. Search visibility (`buildVisibilityClause` in `src/core/search/sql-ranking.ts`) hides soft-deleted pages and archived sources from `searchKeyword` / `searchKeywordChunks` / `searchVector` in both engines. The autopilot cycle's new 9th `purge` phase calls `purgeExpiredSources` + `engine.purgeDeletedPages(72)` so the 72h TTL is real, not honor-system.
- `src/commands/pages.ts` (v0.26.5) — `gbrain pages purge-deleted [--older-than HOURS|Nd] [--dry-run] [--json]` operator escape hatch. Mirror of `gbrain sources purge` for the page-level lifecycle. Hard-deletes pages whose `deleted_at` is older than the cutoff; cascades to content_chunks/page_links/chunk_relations.
- `src/core/op-checkpoint.ts` (v0.36.4.0) — DB-backed checkpoint primitive for long-running ops. Migration v67 introduces `op_checkpoints (op TEXT, fingerprint TEXT, completed_keys JSONB, updated_at TIMESTAMPTZ, PK(op, fingerprint))`. Per-op fingerprint helpers (`embedFingerprint`, `extractFingerprint`, `reindexFingerprint`, `integrityFingerprint`, `purgeFingerprint`) each compute `sha8(canonical-JSON(relevant-params))` so re-running with the same params resumes from `completed_keys` and re-running with different params (e.g. `--limit 100` vs `--limit 200`) starts fresh. Cross-worker safe on Postgres (DB row, no file-lock race); PGLite degrades gracefully. Replaces per-op file-backed JSON checkpoints scattered across `import.ts`, `embed.ts`, `reindex.ts`. The 7-day TTL GC runs in the cycle's `purge` phase. Pinned by `test/op-checkpoint.test.ts` (~15 cases including per-op fingerprint scoping, codex outside-voice review #10-#16). `import-checkpoint.ts` from v0.34.2.0 was NOT migrated to this primitive in v0.36.4.0 — both checkpoint systems coexist without conflict; the migration requires async-propagating 4 sync call sites in `src/commands/import.ts` and rewriting 18 tests, deferred to a follow-up wave.
- `src/core/brain-score-recommendations.ts` (v0.36.4.0) — pure data layer consumed by both `gbrain doctor --remediation-plan` / `--remediate` and `gbrain features`. `computeRecommendations(checks, opts)` returns `Remediation[]` with stable `id`, content-hash `idempotency_key`, `severity`, `est_seconds`, `est_usd_cost`, `depends_on` (D14: references stable ids, not check names — so plan order is reproducible across runs). `classifyChecks(report)` triages every doctor check into `remediable | human_only | blocked` (D13: three-state, not boolean — `human_only` covers RLS warnings and other human-judgment-required gates; `blocked` covers dependency chains where a parent check failed). `maxReachableScore(checks)` computes the ceiling for empty / under-configured brains (no entity pages → graph_coverage caps at 70; no embedding key → embedding_coverage caps at 60). Cost estimates pull from `anthropic-pricing.ts` for synthesize / patterns / consolidate and `embedding-pricing.ts` for embed jobs. Pinned by `test/brain-score-recommendations.test.ts` (~27 cases) including D6 #5 determinism, D9 content-hash idempotency, D12 DB-backed checkpoint provenance, and D13 three-state triage.
- `src/commands/doctor.ts` extension (v0.36.4.0) — new `--remediation-plan` and `--remediate` CLI surfaces. `--remediation-plan [--json] [--target-score N]` prints what would run (stable `id`, `idempotency_key`, `severity`, `est_seconds`, `est_usd_cost`, `depends_on`); `--remediate [--yes] [--target-score N] [--max-usd N]` actually submits each plan step as a Minion job, in dependency order, re-checking score between every step. `--target-score N` defaults to 90; refuses to start when target exceeds `maxReachableScore()` and lists what's missing. `--max-usd N` is the cron-safety guard — submission refuses when the plan's `est_total_usd_cost` exceeds the cap (prevents synthesize loops from burning $100 of Anthropic credits while you're at lunch). JSON envelope adds a `Check.remediation` field (additive, schema_version unchanged). Pinned by tests in `test/doctor.test.ts`.
- `src/commands/jobs.ts` extension (v0.36.4.0) — registers 11 new Minion handlers: `reindex`, `repair-jsonb`, `orphans`, `integrity`, `purge`, `synthesize` (PROTECTED), `patterns` (PROTECTED), `consolidate` (PROTECTED), `extract_facts`, `resolve_symbol_edges`, `recompute_emotional_weight`. Phase wrappers delegate to `runCycle({phases:[name]})` so `src/core/cycle.ts` remains the single source of truth for phase semantics. Same fix wave: the standalone `sync` handler now passes `noExtract: true` to match `runPhaseSync`'s contract — pre-fix, doctor's remediation plan emitting `[sync, extract]` double-extracted (codex #5).
- `src/core/minions/protected-names.ts` extension (v0.36.4.0) — `PROTECTED_JOB_NAMES` extended with `synthesize`, `patterns`, `consolidate`. These phases internally submit `subagent` children with `allowProtectedSubmit=true` and can therefore spend Anthropic credits; treating them as routine "data-quality maintenance" was a misread caught by codex outside-voice (#6). Only trusted local callers (CLI, autopilot, `doctor --remediate`) can submit them; MCP requests are rejected by `submit_job`'s protected-name guard.
- `src/commands/autopilot.ts` extension (v0.36.4.0) — targeted-submit loop replaces blanket `autopilot-cycle` dispatch. Each tick: cheap `engine.getHealth()` (single SQL count) + `computeRecommendations()`, then route by shape — `score >= 95 AND no plan AND <60min since last full` → sleep; `score >= 95 AND >=60min` → submit `autopilot-cycle` (60-min floor exercises phase-coupling invariants on healthy brains); `plan <= 3 steps AND est <5min` → submit individual handlers (targeted); `plan large OR score < 70` → submit full `autopilot-cycle`. The `gbrain-cycle` lock ensures targeted submissions and the full cycle can't run concurrently. `maxWaiting: 1` per submit closes the queue-fan-out vector codex flagged (#17). Pre-fix autopilot ran a full 6-phase cycle every 5 minutes regardless of brain state; healthy brains burned synthesize+patterns+embed cycles for zero work.
- `src/core/cycle.ts` extension (v0.36.4.0) — `purge` phase (the cycle's 9th phase, introduced in v0.26.5 for soft-delete TTLs) extended to GC stale `op_checkpoints` rows older than 7 days. Non-fatal on pre-v67 brains (DROP-target-table check before DELETE).
- `src/commands/embed.ts` extension (v0.36.4.0) — wires `--background` as the reference integration for the new `maybeBackground()` helper. `gbrain embed --stale --background` submits as a Minion job and prints `job_id=N` to stdout, exits 0. Composable in shell pipelines: `JOB=$(gbrain embed --stale --background | grep -oE 'job_id=[0-9]+' | cut -d= -f2); gbrain jobs follow $JOB`. The other six commands (`extract`, `lint`, `backlinks`, `reindex`, `integrity`, `pages`) adopt the same 4-line pattern in a follow-up wave (T7 deferred).
- `src/core/cli-options.ts` extension (v0.36.4.0) — new `maybeBackground(opName, fingerprintArgs, runDirect)` helper. Same semantics in TTY and cron (D9 — no `--no-tty-detect` flag, no surprise behavior change between contexts): when `--background` is passed, submits the op as a Minion job via `op_checkpoints` for resumability and returns the `job_id`. `--background --follow` execs `gbrain jobs follow <id>` so the user sees the same stderr stream they'd get from a direct call. PGLite degrades to inline execution with a clear stderr note ("PGLite worker pool not yet supported; running inline"). Returns a tagged union the caller dispatches on.
- `openclaw.plugin.json` — ClawHub bundle plugin manifest
- `src/commands/capture.ts` + `src/commands/serve-http.ts` + `src/core/{operations,import-file,types,utils,facts/absorb-log,brainstorm/{orchestrator,error-classify},scope,postgres-engine,pglite-engine}.ts` extensions (v0.39.3.0 smoke-test wave) — productionization of the v0.38.0.0 ingestion cathedral release after a real production smoke test against Supabase+PgBouncer (PR #1299, contributed by `@garrytan-agents`). 12 atomic commits closing 2 bugs + 10 warnings: BUG-1 capture frontmatter merge via `mergeCaptureFrontmatter` (uses gray-matter directly, NOT the lossy `parseMarkdown`); BUG-2 `/ingest` null-guard + outer try/catch envelope with `!res.headersSent` guard; WARN-1 dedup via separate normalize-for-hash (`normalizeForHash` strips BOM/CRLF/whitespace/NFKC) + body-after-frontmatter-strip on the DB hash (excludes `captured_at` + `ingested_at` from the existing.content_hash check so capture-cli timestamp variations don't invalidate the chunk cache); WARN-3 friendly `pages_source_id_fk` rewrite via `maybeRewriteSourceFkError` applied to BOTH local + thin-client `callRemoteTool` catch blocks; WARN-4 `facts:absorb` 'No database connection' suppression via typed `instanceof GBrainError && e.problem` check + first-occurrence stack-trace info log (module-scoped `_hasLoggedDisconnectedFactsAbsorb` flag, test seam `_resetFactsAbsorbDisconnectedFlagForTests`); WARN-5 + WARN-6 CLI help discoverability (`capture` added to `CLI_ONLY_SELF_HELP` set + pre-engine-bind `--help` short-circuit in `handleCliOnly` + new `BRAIN` section in `printHelp` text); WARN-7 binary file guard via `detectBinaryNullByte(buf)` first-8KB NUL scan on both `--file` (Buffer-read, no encoding) and `--stdin` (`readStdinBuffer` Buffer accumulator); WARN-8 provenance write-through with put_page accepting 3 new optional params (source_kind, source_uri, ingested_via — `ingested_at` is server-stamped) + CV6 trust gate (when `ctx.remote !== false` IGNORE client params, server stamps `mcp:put_page`, fail-closed posture matches v0.26.9 F7b) + CV12 COALESCE-preserve UPDATE semantics (omitting params on a later put_page preserves prior values; first-write-wins audit trail); WARN-9 `/admin/api/register-client` scopes normalization via new `normalizeScopesInput(raw: unknown)` helper in `src/core/scope.ts` (accepts string, string[], missing; rejects `['read write']` space-in-element bug shape, non-string elements, empty array, unknown scope names; deduped + sorted output); WARN-10 brainstorm timeout surfacing via orchestrator-level try/catch wrap at `runBrainstorm` entry point — covers EVERY internal SQL site by being a single-point wrap, classifies SQLSTATE 57014 (via postgres.js `.code`, alternate `.sqlState`, or message fallback) into `StructuredAgentError` with code='brainstorm_timeout' and hint covering all 3 PG cancel sub-causes (statement_timeout, lock_timeout, user-cancel); CV5 read-path extension surfaces all 4 provenance columns via `getPage` SQL projection + `rowToPage` 3-state optional read + `Page` interface; CV15 canonical source resolver routes capture through `resolveSourceWithTier(engine, parsed.source, cwd)` matching every other CLI op (was `parsed.source ?? 'default'` pre-fix, silently ignoring env/dotfile/local_path tiers); CV7 thin-client `--source` rejection (server-side OAuth client registration owns source scope, per-call override would reopen CV6 spoofing surface); CV3 source_kind taxonomy is now closed (`capture-cli | put_page | mcp:put_page | webhook | file-watcher | inbox-folder | cron-scheduler`), `--source` flag maps to source_id only. Tests: 8 new test files + 3 extended files (test/capture-build-content.test.ts, test/capture-runcapture.test.ts, test/put-page-provenance.test.ts, test/scope-normalize.test.ts, test/cli-help-discoverability.test.ts, test/brainstorm-timeout.test.ts; extended test/facts-absorb-log.test.ts, test/import-file.test.ts, test/e2e/engine-parity.test.ts, test/e2e/serve-http-ingest-webhook.test.ts). Smoke-test report ships verbatim at `docs/v0.38-smoke-test-report.md` with Editor's Note prepending the two factual corrections (BUG-2 actual line + WARN-5 root cause). Plan + 15 decisions + codex outside voice trace at `~/.claude/plans/system-instruction-you-are-working-async-popcorn.md`. v0.39 follow-ups in TODOS.md: SQL-shape rewrite of `listPrefixSampledPages` for PgBouncer, magic-byte allowlist for binary detection, `--source-kind` override flag, ingest_capture handler architecture migration, provenance-history table, facts:absorb root-cause trace.

### BrainBench — in a sibling repo (v0.20+)

BrainBench — the public benchmark for personal-knowledge agent stacks — lives in
[github.com/garrytan/gbrain-evals](https://github.com/garrytan/gbrain-evals). It
depends on gbrain as a consumer; gbrain never pulls in the ~5MB eval corpus or
the pdf-parse dev dep at install time.

gbrain's public API surface (the exports map in `package.json`) is what
gbrain-evals consumes: `gbrain/engine`, `gbrain/types`, `gbrain/operations`,
`gbrain/pglite-engine`, `gbrain/link-extraction`, `gbrain/import-file`,
`gbrain/transcription`, `gbrain/embedding`, `gbrain/config`, `gbrain/markdown`,
`gbrain/backoff`, `gbrain/search/hybrid`, `gbrain/search/expansion`,
`gbrain/extract`. Removing any of these is a breaking change for the
gbrain-evals consumer.

## v0.36.1.0 Hindsight calibration wave (key files cluster)

The wave that taught gbrain to know how the user tends to be wrong + use
that knowledge at every advice surface. Six-migration schema (v67-v72),
three new cycle phases, eight expansions, one admin tab. Plan persisted
at `~/.claude/plans/system-instruction-you-are-working-rippling-knuth.md`.
Convention skill at `skills/conventions/calibration.md` has the agent-
facing rules.

**v0.37.2.0 hotfix (2026-05-20, migration v80)** — `takes_resolution_consistency`
CHECK widened to accept `quality='unresolvable' AND outcome=NULL` as the 4th
valid resolution state. Column-level CHECK on `resolved_quality` renamed to
`takes_resolved_quality_values` and widened to enumerate all 4 states. Unblocks
production grading scripts that write the judge's 4th verdict type. `Take.resolved_quality`,
`TakeResolution.quality`, and `takes-fence.ts:TakeQuality` all widen to 4-state.
`TakesScorecard` gains sibling fields `unresolvable_count` + `unresolvable_rate`;
`resolved` stays 3-state (correct+incorrect+partial) so historical comparisons
hold. `finalizeScorecard` formula: `unresolvable_rate = unresolvable_count / (resolved
+ unresolvable_count)`, NULL when both 0. Spec doc preserved at
`docs/architecture/calibration-quality-gate-spec.md` (from closed PR #1191) since
the follow-up minor (forthcoming) ships the falsifiability + per-category
calibration on top. Migration renumbered v74→v79→v80 during successive master
merges — v0.37.0.0's autonomous-remediation wave claimed v68-v78, then v0.37.1.0
(brainstorm/lsd) claimed v79. Pinned by
R1-R5 in `test/takes-resolution.test.ts` and `test/migrate.test.ts`'s
v80 structural + PGLite round-trip suite (CHECK admits unresolvable+NULL, still
rejects partial+true and unresolvable+true|false, pre-v80 NULL/NULL rows survive).

- `src/core/cycle/base-phase.ts` — abstract `BaseCyclePhase` class.
  Enforces `sourceScopeOpts(ctx)` threading at the type level; closes
  the v0.34.1 source-isolation leak class structurally for every new
  phase. Inherits source-scope, budget meter, error envelope, progress
  reporter. propose_takes / grade_takes / calibration_profile all
  extend it.
- `src/core/cycle/propose-takes.ts` — LLM scans markdown prose,
  proposes gradeable claims to `take_proposals` queue. Idempotency
  cache on `(source_id, page_slug, content_hash, prompt_version)`
  composite unique index. F2 fence-dedup: existing canonical takes
  passed to extractor as context. v0.36.1.0 ships a stub prompt; tuned
  prompt arrives via the T19 synthetic corpus build.
- `src/core/cycle/grade-takes.ts` — walks unresolved takes older than
  6 months, retrieves evidence, asks judge model, caches verdict.
  Auto-resolve DISABLED by default (D17). Conservative thresholds:
  >=0.95 single OR >=0.85 ensemble 3/3 unanimous. T5 ensemble
  (`aggregateEnsemble`) reuses v0.27.x cross-modal substrate; fires on
  borderline 0.6-0.95 band. Writes to `take_grade_cache`.
- `src/core/cycle/calibration-profile.ts` — aggregates resolved takes
  into 2-4 narrative pattern statements + active bias tags. Voice-gated
  via `gateVoice()`. Cold-brain skip when <5 resolved. Writes to
  `calibration_profiles` with audit columns (`voice_gate_passed`,
  `voice_gate_attempts`, `grade_completion`).
- `src/core/calibration/voice-gate.ts` — single `gateVoice()` function
  (D24), mode parameter (`pattern_statement` | `nudge` |
  `forecast_blurb` | `dashboard_caption` | `morning_pulse`). 2 regens
  then hand-written template fallback from
  `src/core/calibration/templates.ts`. Haiku judge with mode-specific
  rubrics; all rubrics structurally forbid clinical/preachy voice.
- `src/core/calibration/cross-brain.ts` — D18 4-rule contract for
  cross-brain calibration reads. Local-first → mount-fallback (only
  with `canReadMountsForCtx(ctx)` true) → cross-brain attribution via
  `source_brain_id` + `from_mount` → subagent prohibition closes the
  OAuth-token-to-cross-brain-leak surface. All 4 rules pinned in
  `test/cross-brain-calibration.test.ts`.
- `src/core/calibration/nudge.ts` — E7 real-time pattern surfacing.
  `evaluateAndFireNudge(opts)` is the full pipeline: threshold check
  (conviction > 0.7, holder match, slug-derived domain hint matches
  active bias tag), cooldown probe (14d via take_nudge_log), fire +
  log. STDERR-only output for v0.36.1.0; multi-channel deferred.
- `src/core/calibration/take-forecast.ts` — E5 Brier-trend at write
  time. Pure math over existing `TakesScorecard`; no LLM. Returns
  `predicted_brier`, `bucket_n`, `overall_brier`. Insufficient-data
  branch at `MIN_BUCKET_N = 5`. `batchForecast` memoizes per
  (holder, domain) tuple.
- `src/core/calibration/gstack-coupling.ts` — E4 outcome-driven
  learnings coupling. `writeIncorrectResolution(opts)` shells out to
  `gstack-learnings-log` binary. Config gate
  (`cycle.grade_takes.write_gstack_learnings`, default false for
  external users). Namespace prefix `gbrain:calibration:v0.36.1.0:` so
  `--undo-wave` can scrub.
- `src/core/calibration/svg-renderer.ts` — D23 server-rendered SVG for
  the admin SPA Calibration tab. Pure functions: data → SVG string.
  Inlines design tokens; XSS-safe via `escapeXml()`. Four chart
  renderers: `renderBrierTrend`, `renderDomainBars`,
  `renderAbandonedThreadsCard`, `renderPatternStatementsCard`. SPA
  renders via `<TrustedSVG>` wrapper behind `requireAdmin`.
- `src/core/calibration/undo-wave.ts` — D18 CDX-3 resolution. `undoWave`
  reverses the wave's mutations: unsets `takes.resolved_*` for
  wave-applied resolutions (cross-checks resolved_by so manual writes
  persist), deletes calibration_profiles, purges nudge logs, marks
  grade-cache rows applied=false. `--dry-run` shows counts without
  writing. Idempotent on wave_version match.
- `src/core/calibration/think-ab.ts` — D19 A/B harness. `runAbTrial`
  calls thinkRunner twice (baseline + with-calibration), records
  preference to `think_ab_results`. `buildAbReport` aggregates over
  30-day window; flags `calibration_net_negative` when n>=20 + win
  rate < 45% on decisive trials.
- `src/core/calibration/recall-footer.ts` — formatter for the morning
  pulse calibration block. Cold-brain branch when <5 resolved. v0.36
  ship state: opt-in via the wiring layer; auto-on in v0.37+.
- `src/core/eval-contradictions/calibration-join.ts` — E3 cross-
  reference. `tagFindingWithCalibration(finding, profile)` returns
  bias-tag context for contradictions that match active patterns.
  Returns null when profile missing (R2 regression — output
  byte-identical to v0.32.6).
- `src/core/think/prompt.ts` extension — E1 anti-bias rewrite.
  `withCalibration` option on `buildThinkSystemPrompt` adds anti-bias
  rules. New `buildCalibrationBlock()` emits the `<calibration>` XML.
  `buildThinkUserMessage` has TWO shapes: default (question first) for
  R1 regression, with-calibration (retrieval → calibration → question
  per D22) when opt-in. Wired into `runThink` via
  `opts.withCalibration` + `opts.calibrationHolder`.
- `src/commands/calibration.ts` — CLI: `gbrain calibration` (read +
  print), `--regenerate`, `--undo-wave <ver>` (T17), `ab-report` (T18).
  MCP op `get_calibration_profile` (scope: read) backs the same data
  path. Source-scoped via `sourceScopeOpts(ctx)`.
- `src/commands/serve-http.ts` extension — three new admin routes:
  `/admin/api/calibration/profile`, `/admin/api/calibration/charts/:type`
  (image/svg+xml; type in {brier-trend, domain-bars,
  pattern-statements, abandoned-threads}), and
  `/admin/api/calibration/pattern/:id` (TD3 drill-down).
- `src/commands/takes.ts` extension — `gbrain takes revisit <slug>`
  (TD4 / D30) opens $EDITOR on the source page with a
  `<!-- gbrain:revisit -->` cursor marker.
- `src/commands/doctor.ts` extension — 4 new checks: `abandoned_threads`,
  `calibration_freshness`, `grade_confidence_drift` (CDX-11 mitigation
  surface; math arrives v0.37+), `voice_gate_health`.
- `admin/src/pages/Calibration.tsx` — Calibration tab. Single-column
  Linear-calm-clarity layout matching the approved variant-B mockup.
  `<TrustedSVG>` wrapper handles `dangerouslySetInnerHTML` for the
  server-rendered SVG.
- `admin/src/index.css` extension — `--text-muted: #555 → #777` (TD2,
  WCAG AA contrast bump from 4.0 to ~5.5 on the #0a0a0f bg).
- `test/fixtures/calibration/extract-takes-corpus/` — synthetic prompt-
  tuning corpus. v0.36.1.0 ships 5 representative pages; full 50-page
  + 10-page holdout generated by `gbrain calibration build-corpus`
  (v0.37+ subcommand). All anonymized per CLAUDE.md placeholder list.
- `scripts/check-synthetic-corpus-privacy.sh` — CDX-14 mitigation. CI
  guard in `bun run verify`. Greps for explicit dollar amounts +
  verifies non-essay fixtures reference at least one placeholder name.
- `test/regressions/v0.36.1.0-iron-rule.test.ts` — R1-R5 regression
  inventory test file. Pins all 5 IRON-RULE regressions in one place
  for future bisects.
- `DESIGN.md` — repo-root design system. Formalizes the de facto admin
  tokens that landed v0.26.0. Calibration target for future
  `/plan-design-review` and `/design-review`.

## Thin-client routing (v0.31.1, Issue #734)

`gbrain init --mcp-only` (v0.29.2) sets up a thin-client install: no local
brain content, just an OAuth client pointing at a remote `gbrain serve --http`.
v0.29.2/v0.30.0 only refused 9 obvious local-only commands; the other ~25
silently fell through to `connectEngine()` and opened the empty local PGLite,
returning "No results." against a populated remote brain. v0.31.1 fixes the
silent-empty-results bug class for every operation surface.

Key files:

- `src/cli.ts` — Routing seam INSIDE the existing op-dispatch path (CDX-1: no
  parallel `src/core/thin-client/` module; routing is a ~80-line conditional
  in `runThinClientRouted`). Detects `isThinClient(cfg)` BEFORE `connectEngine`
  so thin-client installs never open the empty PGLite. localOnly ops on
  thin-client refuse via `refuseThinClient` (with pinpoint hint table
  `THIN_CLIENT_REFUSE_HINTS`). Banner via `printIdentityBannerBestEffort`
  before each routed call (suppressed by `--quiet`, `GBRAIN_NO_BANNER=1`,
  non-TTY default). Exhaustive TS `never` switch on `RemoteMcpError.reason`
  for canned, actionable error messages. ENG-2 renderer parity: local-engine
  path runs `JSON.parse(JSON.stringify(result))` so renderers see the same
  shape on both paths (kills Date/bigint/Buffer drift class).
- `src/core/mcp-client.ts` — `callRemoteTool(config, toolName, args, opts)`.
  Hardened in v0.31.1 (CDX-4): all transport errors normalized to
  `RemoteMcpError` via the `toRemoteMcpError` funnel. New `CallRemoteToolOptions
  {timeoutMs, signal}`; `buildAbortController` composes external signal with
  timeout. New `RemoteMcpErrorReason` stable union, `RemoteMcpErrorDetail.kind`
  ('timeout' | 'aborted' | 'unreachable') sub-tag, `RemoteMcpErrorDetail.code`
  field carrying server-supplied error codes (e.g. `missing_scope`).
  `extractToolErrorCode` parses JSON envelopes first, falls back to substring
  detection for legacy server messages. `unpackToolResult<T>(res)` unchanged
  (parses tool-call JSON content). `_clearMcpClientTokenCache()` test escape.
- `src/core/cli-options.ts` — `parseGlobalFlags` adds `--timeout=Ns` (accepts
  `30s`, `2m`, `500ms`, plain ms). Default `null` = per-command default (30s
  for most ops, 180s for `think`). `parseTimeout(s)` exported helper.
- `src/core/doctor-remote.ts` — `gbrain remote doctor` adds the
  `oauth_client_scopes_probe` check (CDX-5). Probes the read tier via
  `get_brain_identity` and admin tier via `get_health`; reports per-tier
  status with pinpoint remediation when admin is missing. `buildScopeCheck`
  + `ScopeProbeResult` exported for test access. Skippable via
  `GBRAIN_DOCTOR_SKIP_SCOPE_PROBE=1` for fixtures that mock /mcp at JSON-RPC
  initialize level only (MCP SDK Client hangs on shape mismatch).
- `src/core/ssrf-validate.ts` (v0.36 Commit 0) — DNS-rebinding-defended URL validation. `validateAndResolveUrl(url)` resolves the hostname via `dns.lookup({all: true, family: 0})`, checks EVERY A AND AAAA record against the internal-IP deny list, returns the resolved IP so callers fetch by IP (defeats DNS rebinding: validation IP === fetch IP). `fetchWithSSRFGuard(url, opts)` does redirect-aware fetching with per-hop re-validation, max 3 hops by default. Reusable across all URL-fetching features. Test seam `__setDnsLookupForTests` for hermetic tests.
- `src/core/search/query-intent.ts` extension (v0.36 cross-modal wave) — new `suggestedModality: 'text' | 'image' | 'both'` axis on `QuerySuggestions`. Module-scope `CROSS_MODAL_PATTERNS` regex array (compiles once at module load). `isAmbiguousModalityQuery(query)` heuristic gate fires when a visual noun + reference marker combination indicates genuinely ambiguous routing — used by the Commit 4 LLM tie-break to bound LLM calls to <1% of queries.
- `src/core/search/mode.ts` extension (v0.36 cross-modal wave) — `ModeBundle` extended with 7 cross-modal knobs: `cross_modal_both_text_weight` / `cross_modal_both_image_weight` (D6 weighted RRF for `'both'` mode, defaults 0.6/0.4), `image_query_text_refinement_weight` / `image_query_image_refinement_weight` (D13 hybrid intersect for `searchByImage` query refinement, defaults 0.4/0.6), `unified_multimodal` + `unified_multimodal_only` (Phase 3 unified column routing flags), `cross_modal_llm_intent` (Commit 4 opt-in escalation). `SEARCH_MODE_CONFIG_KEYS` extended with 7 corresponding config keys. `KNOBS_HASH_VERSION` bumped 2→3 (D2 — closes the silent cache-hit class where a cached text-mode result could leak to an image-mode caller).
- `src/core/search/hybrid.ts` extension (v0.36 cross-modal wave) — cross-modal routing branch at the embed step. Resolves `effectiveModality` from per-call `opts.crossModal` (normalized: literal `'auto'` → undefined per D22-1) → `suggestions.suggestedModality` → `'text'` default. Image route: `embedQueryMultimodal` + `searchVector({embeddingColumn: 'embedding_image'})`, skip expansion + keyword (D9 mode-bundle override). 'both' route: parallel text + image vector searches merged via `rrfFusionWeighted` with `effectiveRrfK(baseRrfK, weight)` from the configured cross-modal weights. Phase 3 unified routing fires when `cfg.search.unified_multimodal === true` — bypasses dual-column branching, runs `embedQueryMultimodal` + `searchVector({embeddingColumn: 'embedding_multimodal'})`, D8 fail-open on zero rows + not strict-mode falls through to dual-column. Commit 4 LLM escalation fires only when (no explicit per-call opt) AND (regex returned 'text') AND (`cfg.search.cross_modal.llm_intent` is true) AND (`isAmbiguousModalityQuery` returns true). Fail-open on every error.
- `src/core/search/image-loader.ts` (v0.36 Phase 2) — `loadImageInput(input, opts)` accepts local path, `data:` URI, or `http(s)://` URL. Magic-byte sniff for PNG/JPEG/WebP. Hard size cap (default 10 MB, configurable via `search.image_query.max_bytes`). For URLs: routes through `fetchWithSSRFGuard` so DNS rebinding + redirect chains are defeated. Pre-flight Content-Length check + post-fetch size guard for lying servers. `ImageLoadError` with discriminated `code` (INVALID_FORMAT / OVERSIZED / INVALID_URL / FETCH_FAILED / TIMEOUT / SSRF_BLOCKED / NOT_FOUND).
- `src/core/search/by-image.ts` (v0.36 Phase 2) — `searchByImage(engine, input, opts)`. Always runs image branch (`embedQueryMultimodalImage` + `searchVector(embedding_image)`). D13 hybrid intersect: when caller provides optional `query`, runs parallel text branch via `embedQueryMultimodal(query)` and merges via `rrfFusionWeighted` with weights from resolved mode. Phase 3 widens to unified column once `search.unified_multimodal=true` (transparently upgrades the retrieval quality post-reindex).
- `src/core/spend-log.ts` (v0.36 Phase 2 D23-#6) — per-OAuth-client paid-API spend tracking against the `mcp_spend_log` table (migration v74). `checkBudget(engine, clientId, capCents)` is the pre-flight gate; throws `BudgetExceededError` when today's spend has hit the cap. `recordSpend(engine, entry)` is best-effort post-call. UTC day-aligned aggregation so caps roll over deterministically regardless of server timezone. Local CLI callers (no clientId) bypass the gate. Pre-v0.36 brains without the table fail open to spend=0. `VOYAGE_MULTIMODAL_3_PER_IMAGE_CENTS` = 0.12 cents per image embed.
- `src/core/search/llm-intent.ts` (v0.36 Commit 4) — opt-in LLM tie-break. `classifyModalityWithLLM(query, fallback)` routes through `gateway.chat()` with a fixed single-word-output system prompt. 1s timeout via AbortController. `parseModality(raw, fallback)` is the pure parser — tolerates trailing punctuation + casing. Fail-open on every error (gateway unavailable, timeout, parse failure, unrecognized output) — returns fallback so a misbehaving LLM can never break search. Cost-bounded by the ambiguity heuristic in `query-intent.ts` (fires <1% of queries when on).
- `src/commands/reindex-multimodal.ts` (v0.36 Phase 3) — `gbrain reindex --multimodal [--limit N] [--dry-run] [--cost-estimate] [--no-embed] [--yes] [--json]`. Walks `content_chunks WHERE embedding_multimodal IS NULL`, batches via `embedMultimodalSafe` (Commit 0 partial-failure-aware), persists. D7 lock acquisition via `tryAcquireDbLock('gbrain-reindex-multimodal', 360min)`. Cost prompt + 10s Ctrl-C grace window in TTY. `GBRAIN_NO_REEMBED=1` bypass. Checkpoint at `~/.gbrain/reindex-multimodal-checkpoint.json` for resume. D23-#2 auto-flip prompt at coverage=100% completion (TTY: interactive; non-TTY: stderr hint with paste-ready command).
- `src/core/backfill-registry.ts` extension (v0.36) — new `modality` backfill kind. SQL filter requires `chunk_source='image_asset'` AND `embedding_image IS NOT NULL` AND `(modality IS NULL OR modality != 'image')`. D22-7 defensive guard: never flag a non-image chunk that happens to have `embedding_image` populated. Idempotent — second run finds zero rows.
- `src/core/migrate.ts` v74 (`mcp_spend_log`) + v75 (`embedding_multimodal_column`) — Phase 2 spend-log table + Phase 3 unified column ALTER. v75 is column-only (no HNSW index — deferred to post-reindex per pgvector best practice). v74 uses BTREE on `(client_id, created_at)` + `(token_name, created_at)` — `date_trunc('day', TIMESTAMPTZ)` is NOT IMMUTABLE so can't appear in index expressions; range scan on created_at covers the per-day rollup query.
- `src/core/operations.ts` — `get_brain_identity` op (read scope, no params,
  banner-only): cheap counter packet `{version, engine, page_count,
  chunk_count, last_sync_iso}` for the thin-client identity banner. Reuses
  `engine.getStats()`; banner's 60s client-side TTL bounds frequency to
  ≤1/60s per CLI process (well below the Fly.io health-check cadence that
  motivated the original `getStats` cost warning).
- `src/commands/{salience,anomalies,graph-query,think}.ts` — Per-command
  thin-client routing branches. These commands bypass the operation-layer
  dispatch in cli.ts (call `engine.foo()` directly), so each gets its own
  `if (isThinClient(cfg)) { callRemoteTool(...) }` branch that maps CLI flags
  to op params. `think` is a special case: the server's `think` op
  intentionally disables `--save`/`--take` for remote callers
  (operations.ts:1103-1135 trust-boundary gate); thin-client `think` warns
  loudly when those flags are set.

## Schema Cathedral v3 (v0.40.7.0)

The schema-pack mutation surface shipped in v0.40.7.0 as the production rebuild of
closed community PR #1321 (`@garrytan-agents`). Six new foundation modules + a
mutate skeleton + stats/sync data plane + 14 CLI verbs + 9 MCP ops + a first-class
agent skill. See `~/.claude/plans/system-instruction-you-are-working-recursive-thacker.md`
for the full plan + 21 captured design decisions.

Key files (v0.40.7.0 additions):
- `src/core/schema-pack/pack-lock.ts` — Atomic `O_CREAT|O_EXCL` per-pack lock. DELIBERATELY NOT the `existsSync + writeFileSync` TOCTOU shape from `src/core/page-lock.ts` (codex C8 caught the bug class). Default 60s TTL, refresh every 10s while `withPackLock(fn)` runs, `--force` semantics = "steal stale lock" NOT "skip locking." Lock path per-pack so two packs never block each other.
- `src/core/schema-pack/mutate-audit.ts` — ISO-week JSONL at `~/.gbrain/audit/schema-mutations-YYYY-Www.jsonl`. Privacy-redacted per D20: type names → sha8, prefixes → first slug segment only, matches `candidate-audit.ts` privacy posture. Logs BOTH success AND failure events so the v0.40.7+ `schema_pack_writability` doctor check has signal to read. `summarizeMutations()` is the cross-surface parity primitive.
- `src/core/schema-pack/registry.ts` extensions — `invalidatePackCache(name?)` walks the extends-chain reverse-graph (codex C6 fix; pre-v0.40.7, editing a parent pack silently left children stale). `tryCachedPack(name)` TTL-gated fast path: inside `STAT_TTL_MS` (default 1000ms, env `GBRAIN_PACK_STAT_TTL_MS`) returns cached without statting. Outside the window: stats every file in the chain; cascade-invalidates on mtime change (D11 cross-process detection).
- `src/core/schema-pack/best-effort.ts` — `loadActivePackBestEffort(ctx)` returns `ResolvedPack | null`. Single source of truth for the T1.5 wiring sites. `null` means EMPTY FILTER (NOT hardcoded defaults — D4 contract closing the silent-violation bug class).
- `src/core/schema-pack/lint-rules.ts` — 12 pure rule functions. `withMutation`'s pre-write validation gate composes the 10 file-plane rules; the 2 DB-aware rules (`extractable_empty_corpus`, `mutation_count_anomaly`) need an engine. Single source of truth consumed by CLI lint + MCP `schema_lint` + the pre-write validation gate. **v0.41.37.0 (#1569):** new file-plane rule `link_regex_catastrophic_backtrack` — advisory ReDoS pre-screen that flags the classic nested-quantifier shapes (`(a+)+`, `(a*)*`, `(a+)*`, `(\w+)+`) in a link_type's `inference.regex` via `NESTED_QUANTIFIER_RE`. WARNING not error: a hard reject would disable the whole pack on upgrade (pages fall back to legacy typing). The runtime input-length cap in `redos-guard.ts` is the actual safety net; this rule tells the pack author to fix the pattern.
- `src/core/schema-pack/redos-guard.ts` + `src/core/schema-pack/link-inference.ts` (v0.41.37.0, #1569) — ReDoS hardening for pack inference regexes. `redos-guard.ts` adds `MAX_REGEX_INPUT_CHARS` (default 64_000, env override `GBRAIN_MAX_REGEX_INPUT_CHARS`) — a hard input-length cap, the real runtime safety net (catastrophic backtracking needs a long input to blow up; a link-extraction `context` is normally a sentence or short paragraph). Over the cap, `runRegexBounded` throws the new tagged `RegexInputTooLargeError` and the regex is skipped (degrade-to-mentions) without entering the `node:vm`. `link-inference.ts:inferLinkTypeFromPack` no-budget branch (test contexts) previously ran `new RegExp(pattern).test(context)` UNBOUNDED — the one ReDoS hole with no timeout; it now routes through `runRegexBounded` so the input-length cap + per-regex vm timeout (`PER_REGEX_TIMEOUT_MS = 50`) apply on every path. Defensive hardening + diagnostics; the deterministic ~3100-file sync-wedge root cause remains open (no repro). Pinned by `test/redos-hardening.test.ts` + `test/schema-pack-lint-rules.test.ts`.
- `src/core/schema-pack/query-cache-invalidator.ts` — `invalidateQueryCache(engine, sourceId?)` DELETEs query_cache rows so cached search results bound to old page types don't survive a schema mutation. Codex C9 fix.
- `src/core/schema-pack/mutate.ts` — 8-step `withMutation` skeleton (bundled-guard → lock → read → mutator → validate → atomic write → audit → invalidate). 11 mutation primitives: `addTypeToPack`, `removeTypeFromPack` (with codex C14 reference check), `updateTypeOnPack`, `addAliasToType`, `removeAliasFromType`, `addPrefixToType`, `removePrefixFromType`, `addLinkTypeToPack`, `removeLinkTypeFromPack`, `setExtractableOnType`, `setExpertRoutingOnType`. Atomic write via `.tmp + fsync + rename` — pack file on disk is NEVER partial. Inline minimal JSON→YAML emitter so YAML packs stay YAML (does NOT preserve comments — pin pack.json if you care about layout).
- `src/core/schema-pack/stats.ts` — `runStatsCore(engine, opts)` returns per-source + aggregate page counts + coverage % + `dead_prefixes` (declared prefixes with zero matching pages — agent's drilldown signal). Multi-source aware (`sourceIds[]` federated, `sourceId` single, or whole-brain). PGLite + Postgres parity via `executeRaw`. Empty brain → coverage:1.0 (vacuous truth).
- `src/core/schema-pack/sync.ts` — `runSyncCore(engine, opts)` chunked UPDATE in 1000-row batches per declared prefix (D14). Concurrent writers never block on a single row >100ms. Codex C5 write-side scoping via `ctx.sourceId` directly (NOT `sourceScopeOpts` which inherits OAuth read federation). Idempotent on `--apply` re-run.
- `src/commands/schema.ts` extension — 14 new CLI verbs in the dispatch table: `add-type`, `remove-type`, `update-type`, `add-alias`, `remove-alias`, `add-prefix`, `remove-prefix`, `add-link-type`, `remove-link-type`, `set-extractable`, `set-expert-routing`, `stats`, `sync`, `reload`. `withConnectedEngine` defensive fix from closed PR #1321 retained. Lifecycle-grouped help text (Inspection / Activation / Authoring / Discovery+repair).
- `src/core/operations.ts` extension — 9 new MCP ops: `get_active_schema_pack`, `list_schema_packs`, `schema_stats`, `schema_lint`, `schema_graph`, `schema_explain_type`, `schema_review_orphans` (all read-scope, NOT localOnly), plus `schema_apply_mutations` (**admin scope, NOT localOnly per D2** so remote agents like your OpenClaw can author packs over HTTPS MCP — batched per D10, one MCP tool taking an `mutations[]` array atomically inside ONE `withPackLock`, audit log captures `actor: mcp:<clientId8>`) and `reload_schema_pack` (admin, NOT localOnly). Trust posture: per-call `schema_pack` opt STAYS rejected for remote callers via `op-trust-gate.ts` (R2 regression preserved).
- `src/commands/whoknows.ts` + `src/core/operations.ts:find_experts` — T1.5 wiring sites. Pack-aware via `expertTypesFromPack(pack.manifest)` from `best-effort.ts`. Pack-load failure → EMPTY filter (NOT hardcoded `['person', 'company']` defaults per D4). A `researcher` type declared `--expert` now surfaces in `whoknows` results; pre-v0.40.7 it silently never matched.
- `skills/schema-author/SKILL.md` — Agent dispatcher for "evolve the schema pack." Triggers: 15+ phrasings including "add a page type", "my brain has untyped pages", "propose new types from my corpus", "backfill page types". Explicit Non-goals callout to `brain-taxonomist` (files one page) and `eiirp` (schema-check during iteration) so agents pick the right surface. 7-phase workflow: brain → assess → propose → apply → sync → verify → commit. Lists every gbrain schema CLI verb + every MCP op the skill uses. `brain_first: exempt` frontmatter. Required v0.40.7+ conformance sections: Contract, Anti-Patterns, Output Format.
- `skills/conventions/schema-evolution.md` — Canonical convention: "when to add a type vs alias vs prefix." Decision tree: <20 pages → don't pack-codify; 20-100 → alias or narrow prefix on existing type; 100+ → first-class type. Don'ts section + "when to remove a type" + "when to commit the pack" all answered in one place.
- `skills/RESOLVER.md` + `skills/manifest.json` — schema-author wired into the dispatcher with full functional-area trigger list (compressed routing pattern per v0.32.3 dispatcher convention).

T1.5 wiring is partial in v0.40.7.0. Three follow-ups filed in TODOS.md under
"v0.40.7.0 Schema Cathedral v3 follow-ups (v0.40.7+)" — enrichment-service.ts
union widening (`'person' | 'company'` → `string`), facts/eligibility.ts
pack-aware `ELIGIBLE_TYPES` wiring, and 3 doctor checks (schema_pack_coverage,
schema_pack_writability, schema_pack_mutation_audit).

## Commands

Run `gbrain --help` or `gbrain --tools-json` for full command reference.

Key commands added in v0.7:
- `gbrain init` — defaults to PGLite (no Supabase needed), scans repo size, suggests Supabase for 1000+ files
- `gbrain migrate --to supabase` / `gbrain migrate --to pglite` — bidirectional engine migration

Key commands added for Minions (job queue):
- `gbrain jobs submit <name> [--params JSON] [--follow] [--dry-run]` — submit a background job. v0.13.1 adds first-class flags for every `MinionJobInput` tuning knob: `--max-stalled N`, `--backoff-type fixed|exponential`, `--backoff-delay Nms`, `--backoff-jitter 0..1`, `--timeout-ms N`, `--idempotency-key K`.
- `gbrain jobs list [--status S] [--queue Q]` — list jobs with filters
- `gbrain jobs get <id>` — job details with attempt history
- `gbrain jobs cancel/retry/delete <id>` — manage job lifecycle
- `gbrain jobs prune [--older-than 30d]` — clean old completed/dead jobs
- `gbrain jobs stats` — job health dashboard
- `gbrain jobs smoke [--sigkill-rescue]` — health smoke test. `--sigkill-rescue` is the v0.13.1 regression guard for #219: simulates a killed worker and asserts the stalled job is requeued instead of dead-lettered on first stall.
- `gbrain jobs work [--queue Q] [--concurrency N]` — start worker daemon (Postgres only)

Key commands added in v0.40.3.0 (contextual retrieval + cache gate + 4 CLI verbs):
- `gbrain mounts enable <id>` / `disable <id>` — toggle a mount without removing it.
- `gbrain mounts trust-frontmatter <id>` / `untrust-frontmatter <id>` — let a mounted brain's per-page `contextual_retrieval_mode` frontmatter override the source default. Off by default for mounts (security posture per D15); host source is always trusted.
- `gbrain sources set-cr-mode <id> <none|title|per_chunk_synopsis>` — per-source contextual retrieval mode override. Pass `unset` or `default` to clear (NULL falls through to global). Missing source ID fails loudly with paste-ready `gbrain sources list` hint.
- `gbrain config set search.mode tokenmax` triggers a mode-switch banner explaining the per-chunk Haiku synopsis backfill cost, and (on TTY + active Minion worker) offers to submit `gbrain reindex --markdown` as a Minion job. Non-TTY callers get a paste-ready hint to stderr instead of a silent stall. Suppress with `GBRAIN_NO_MODE_SWITCH_UX=1` for CI fixtures.
- Cache invalidation gate is now two-layer (per D11 codex finding): Layer 1 cheap MAX(generation) bookmark via `pages_generation_idx`, Layer 2 per-page snapshot via jsonb_each + LEFT JOIN pages. Pre-v0.40.3.0 cache rows with empty `{}` snapshot are vacuously valid (IRON-RULE backward compat).
- KNOBS_HASH_VERSION bumped 3 → 5 (skipped past 4 reserved by salem's v0.40.4 graph-signals work). One-time cache-row invalidation on upgrade; refills within TTL.
- Three new Minion handlers wired into RemediationStep consumer pattern: `lint-fix`, `integrity-auto`, `sync-retry-failed`. Thin wrappers around already-shipping CLI commands; NOT in PROTECTED_JOB_NAMES (idempotent, no shell exec, MCP-safe). `sync-skip-failed` deliberately NOT in this set per codex D12 Bug 3.
- `src/core/remediation-step.ts` (NEW canonical module) exports RemediationStep type + makeRemediationStep factory + canonical-JSON idempotencyKey() per codex D12 Bug 2. Future doctor checks emit RemediationSteps via the factory instead of hand-rolling the shape.
- `src/core/search/query-cache-gate.ts` (NEW) exports `buildPageGenerationsSnapshot(engine, pageIds)` + `CACHE_GATE_WHERE_CLAUSE` SQL fragment + `validateCacheRowAgainstPages()` pure validator. **v0.41.25.0 (codex outside-voice on /plan-eng-review):** Layer 1 bookmark read source switched from `MAX(generation) FROM pages` to `SELECT value FROM page_generation_clock WHERE id = 1` at both store + lookup sites. Closes two pre-existing silent stale-cache bug classes that were independent of any sync work: (1) CDX-2 — UPDATE to a non-max page set `NEW.generation = OLD.generation + 1` which didn't advance MAX, so cache silently served stale on every non-max UPDATE; (2) CDX-1 — DELETE didn't fire the row-level trigger at all, and even an AFTER DELETE wouldn't move MAX because surviving rows are untouched. The new clock is bumped per-statement by `bump_page_generation_clock_trg` (statement-level trigger created in migration v106) so every INSERT/UPDATE/DELETE statement advances the bookmark exactly once regardless of row cardinality (D19 — per-row would turn a 73K-row batch DELETE into 73K UPDATEs on the same counter). Also CDX-6/D20 fix: empty-result cache rows used to be "vacuously valid" via Layer 2's `qc.page_generations = '{}'::jsonb` shortcut, silently serving stale empty results across subsequent matching INSERTs. The shortcut is gone — empty snapshots now require Layer 1 to pass. `CACHE_GATE_WHERE_CLAUSE` enforces `qc.page_generations <> '{}'::jsonb` AND the per-page check (not OR). One-time post-upgrade cache miss spike on legacy `{}` rows is acceptable — the cache fills back up correctly and the clock seed `COALESCE(MAX(pages.generation), 0)` keeps non-empty legacy rows serving until the next write. Pinned by 5 new cases in `test/page-generation-counter.test.ts` (CDX-1/CDX-2/CDX-6 regressions + statement-level-trigger-fires-once contract) and 2 new e2e cases in `test/e2e/cache-gate-pglite.test.ts`. The existing pre-v0.41.25.0 `vacuously valid legacy row` IRON-RULE assertion in both files is intentionally inverted: that path was the CDX-6 bug.
- `src/core/search/mode-switch-ux.ts` (NEW) exports `summarizeTransition()` 5-cell matrix + `probeWorkerAvailable()` worker liveness proxy via minion_jobs activity + `buildReindexIdempotencyKey()` content-stable key + `runModeSwitchUx()` orchestrator.

Key commands added in v0.41.31.0 (embedding cost-model + stale-semantics wave):
- `gbrain sync --all` cost gate is now mode-aware. When embedding is DEFERRED (federated_v2 parallel path → per-source `embed-backfill` jobs), the gate is INFORMATIONAL — it prints the backfill cap, the current backlog cost, and the count of queued backfill jobs, and NEVER exits 2. When embedding runs INLINE (v2 off, or `--serial` without `--no-embed`), the gate BLOCKS only when the NEW-CONTENT estimate exceeds the floor. Cost previews now name the ACTUALLY-configured embedding model and price at its real rate (no more hardcoded OpenAI over-statement on cheaper models).
- `gbrain config set sync.cost_gate_min_usd <USD>` — inline-path cost-gate floor (DB plane, default `$0.50`). Below this estimate the inline `sync --all` gate proceeds without blocking, killing the noise where a tiny incremental sync prompted on every cron. Set to `0` to block on any nonzero inline cost. Fail-open to the default on a missing/invalid value.
- `gbrain embed --stale` now re-embeds pages whose embedding model/dimensions changed, not just pages with NULL embeddings. After a model or dims swap, the stored `pages.embedding_signature` differs from the current one, so the next `embed --stale` (or per-source `embed-backfill` job) invalidates and re-embeds those pages. GRANDFATHER: pages embedded before v0.41.31.0 have a NULL signature and are NEVER flagged stale, so the upgrade does NOT trigger a whole-corpus re-embed. `embed --stale --dry-run` counts signature-drift without mutating.
- `gbrain sources status` gains a `BACKFILL` column (`active(N)` / `queued(N)` / `idle`) between `EMBED` and `FAILS` so an operator can see deferred embedding work after `sync --all` exits 0.

Key commands added in v0.36.4.0 (brain-health-100 wave):
- `gbrain doctor --remediation-plan [--target-score N] [--json]` — preview the dependency-ordered plan that would drive the brain to target. JSON envelope is stable: each `Remediation` carries `id`, `idempotency_key` (content-hash for cron-safe retries), `severity`, `est_seconds`, `est_usd_cost`, and `depends_on` (referencing other ids). Empty `recommendations` array when the brain is already at target.
- `gbrain doctor --remediate [--yes] [--target-score N] [--max-usd N]` — actually submit the plan. Walks dependency order, submits one Minion job per step, re-checks score between steps, refuses to spend past `--max-usd` (defaults: target=90, max-usd=infinite — but cron callers should always pass `--max-usd`). Bails when target exceeds `maxReachableScore()` for the brain (empty / under-configured brains) with a clear list of what's missing.
- `gbrain embed --stale --background` — submit the embed sweep as a Minion job; print `job_id=N` to stdout; exit. Composable in shell pipelines. Add `--background --follow` to attach to the job's stderr stream (same UX as a direct call).
- Eleven new Minion job types submittable via `gbrain jobs submit <name>`: `reindex`, `repair-jsonb`, `orphans`, `integrity`, `purge`, `synthesize` (PROTECTED), `patterns` (PROTECTED), `consolidate` (PROTECTED), `extract_facts`, `resolve_symbol_edges`, `recompute_emotional_weight`. PROTECTED ones reject MCP submission and require `--allow-protected` from a trusted local caller (CLI, autopilot, `doctor --remediate`).
- `gbrain autopilot` (existing daemon) is now health-aware. Tick cost on a healthy brain drops from "full 6-phase cycle every 5 minutes" to "one SQL count, then sleep". Degraded brains get targeted handlers (`[sync]`, `[embed]`, `[backlinks]`) instead of the full cycle when the plan is small; large plans still get `autopilot-cycle`. The "60-minute full-cycle floor" runs the full phase set on a healthy brain at least every hour so phase-coupling invariants (lint-first, synthesize-before-patterns, embed-after-consolidate) keep getting exercised.

Key commands added in v0.32.7 (CJK fix wave):
- `gbrain reindex --markdown [--limit N] [--dry-run] [--json] [--no-embed] [--repo PATH]` — operator-facing markdown re-chunk sweep. Walks pages with `chunker_version < MARKDOWN_CHUNKER_VERSION` (currently 2) and re-imports each with `forceRechunk: true` so the new chunker shape actually applies. Run automatically by `gbrain upgrade`'s post-upgrade hook; available manually for triage.
- `gbrain doctor` learns a new `slug_fallback_audit` check: surfaces info-severity entries from `~/.gbrain/audit/slug-fallback-YYYY-Www.jsonl` (last 7 days) as an `ok` count when CJK / emoji / exotic-script filenames imported via the frontmatter-slug fallback path.
- `gbrain search "<CJK substring>"` on PGLite brains now uses an `ILIKE`-based fallback with bigram-frequency-count ranking when the query contains Han / Hiragana / Katakana / Hangul Syllables. ASCII queries continue through `websearch_to_tsquery('english')` unchanged. Postgres-side CJK FTS still requires an extension (pgroonga / zhparser) — see v0.33+ TODO.
- `gbrain upgrade` post-upgrade flow now prints a cost estimate before re-embedding: `[chunker-bump] Will re-embed ~N markdown pages via <provider:model>, est. ~$X.XX, ~Ymin. Press Ctrl-C within 10s to abort.` Sourced from real SQL counts + char totals; TTY-only wait (non-TTY auto-proceeds for CI / cron). Env overrides: `GBRAIN_NO_REEMBED=1` bails out entirely with a doctor-warning marker; `GBRAIN_REEMBED_GRACE_SECONDS=0` skips the wait.

Key commands added in v0.33.1.1 (Voyage 2048-dim correctness wave):
- `gbrain models doctor` learns a new zero-token `embedding_config` probe that runs FIRST, before any chat/expansion probes spend money. Catches Voyage flexible-dim misconfigs at config time, not first-embed: `embedding_model: voyage:voyage-4-large` with `embedding_dimensions` outside `{256, 512, 1024, 2048}` (most commonly: `embedding_dimensions` left unset, falling back to the OpenAI default 1536 which Voyage rejects with an opaque HTTP 400). Surfaces a paste-ready `gbrain config set embedding_dimensions <256|512|1024|2048>` fix in both human and JSON output. New probe status `'config'` joins `{ok, model_not_found, auth, rate_limit, network, unknown}`; new touchpoint label `'embedding_config'` joins `'chat'` and `'expansion'`.
- Voyage 2048-dim brains now actually embed at 2048 dims. `embedding_model: voyage:voyage-4-large` + `embedding_dimensions: 2048` routes through the SDK-supported `dimensions` field, which `voyageCompatFetch` translates to Voyage's `output_dimension` on the wire. Same fix covers `voyage-3-large`, `voyage-3.5`, `voyage-3.5-lite`, `voyage-4`, `voyage-4-lite`, `voyage-code-3`. `voyage-4-nano` (open-weight, fixed 1024-dim) intentionally NOT in the flexible-dim allowlist — sending `output_dimension` to nano's endpoint produces an error.
- Runtime validator: `dimsProviderOptions()` throws `AIConfigError` at the embed boundary with a paste-ready fix hint when a Voyage flexible-dim model is configured with an invalid dim — fail-loud even if you skipped `gbrain models doctor`.
- `VoyageResponseTooLargeError` (new tagged class exported from `src/core/ai/gateway.ts`): the 256 MB per-response cap inside `voyageCompatFetch` was previously throwing a generic `Error` that the surrounding parse-error try/catch silently swallowed, returning the oversized response to the AI SDK anyway. Now thrown at both cap sites (Content-Length Layer 1, per-embedding base64 Layer 2) and rethrown from the catch via `instanceof` check — the cap is now actually effective.

Key commands added in v0.31.12 (model tier system + routing CLI):
- `gbrain models [--json]` — read-only routing dashboard. Prints the four tier defaults (`utility`/`reasoning`/`deep`/`subagent`), the resolved value for each (after re-walking `models.default` → `models.tier.<tier>` → env → `TIER_DEFAULTS`), every per-task override (`models.dream.synthesize`, `models.dream.patterns`, `models.drift`, `models.auto_think`, `models.think`, `models.subagent`, `facts.extraction_model`, `models.eval.longmemeval`, `models.expansion`, `models.chat`, `models.dream.synthesize_verdict`), the alias map (defaults + user overrides), and a source-of-truth column (`default` / `config: <key>` / `env: <VAR>`).
- `gbrain models doctor [--skip=<provider>] [--json]` — 1-token reachability probe against each configured chat + expansion model. Classifies failures into `{model_not_found, auth, rate_limit, network, unknown}`. The structural fix for the bug class that motivated v0.31.12 (v0.31.6's `claude-sonnet-4-6-20250929` chat default 404'd silently on every install).
- Power-user model routing via config keys:
  - `gbrain config set models.default opus` — route every internal call (chat, expansion, synthesis, classification) through Opus 4.7. Subagent loop still falls back to `claude-sonnet-4-6` automatically (Anthropic-only by construction).
  - `gbrain config set models.tier.<tier> <model>` — override one tier independently (`utility` / `reasoning` / `deep` / `subagent`).
  - `gbrain config set models.aliases.frontier anthropic:claude-opus-4-7` — define an alias, then `gbrain config set models.default frontier`.
  - Per-task keys (e.g. `gbrain config set models.dream.synthesize <model>`) still beat tier overrides because they are more specific.
- New `subagent_provider` check in `gbrain doctor` surfaces config drift if `models.tier.subagent` or `models.default` would route the Anthropic Messages API tool-loop to a non-Anthropic provider.
- The skill at `skills/conventions/model-routing.md` was rewritten to cover both the new tier system AND the existing subagent spawn routing in one canonical doc (power-user recipes, three-layer enforcement explanation, override priority chain).

Key commands added in v0.28.1 (LongMemEval in the box):
- `gbrain eval longmemeval <dataset.jsonl>` — run the public LongMemEval benchmark against gbrain hybrid retrieval. Flags: `--limit N`, `--model M`, `--retrieval-only`, `--keyword-only`, `--expansion`, `--top-k K`, `--output FILE`. One in-memory PGLite per benchmark run; `TRUNCATE` between questions over runtime-enumerated `pg_tables` (schema-migration-safe); `~/.gbrain` never opened. `--expansion` defaults OFF (deterministic, no per-query Haiku). Default model resolves through `resolveModel()` 6-tier chain with new `models.eval.longmemeval` config key. `gbrain eval longmemeval --help` works without a configured brain (hermeticity gate).
- Sanitization parity with takes: `INJECTION_PATTERNS` exported from `src/core/think/sanitize.ts`. The benchmark harness re-uses the same pattern set so adding a new injection pattern automatically covers takes AND benchmarks.
- Hand the resulting JSONL to LongMemEval's published `evaluate_qa.py` to score (not bundled — needs OpenAI gpt-4o per their spec). Dataset: https://huggingface.co/datasets/xiaowu0162/longmemeval.

Key commands added in v0.26.5 (destructive-guard, end-to-end):
- `gbrain sources archive <id>` — soft-delete a source. Hides from search via the new `sources.archived` column + cascading visibility filter. Preserves data for 72h. (PR #595 cherry-pick.)
- `gbrain sources restore <id> [--no-federate]` — un-archive a soft-deleted source. Re-federates by default.
- `gbrain sources archived [--json]` — list soft-deleted sources with their TTL.
- `gbrain sources purge [<id>] [--confirm-destructive]` — permanent delete; with no id, purges all sources whose TTL expired.
- `gbrain sources remove <id> [--confirm-destructive] [--dry-run]` — `--yes` alone no longer enough on populated sources. Boxed impact preview before destruction.
- `gbrain pages purge-deleted [--older-than HOURS|Nd] [--dry-run] [--json]` — operator escape hatch for page-level soft-delete cleanup. Mirror of `gbrain sources purge`. The autopilot cycle's new `purge` phase calls the same library function automatically every run.
- MCP `delete_page` op semantically shifts from hard-delete to soft-delete. New ops: `restore_page` (`scope: write`), `purge_deleted_pages` (`scope: admin`, `localOnly: true`).
- `get_page` and `list_pages` extended with `include_deleted: boolean` (default false).
- New autopilot cycle phase `purge` (9th, runs after `orphans`). `gbrain dream --phase purge` runs only the purge sweep.
- Index strategy note: the partial index `pages_deleted_at_purge_idx ON pages (deleted_at) WHERE deleted_at IS NOT NULL` supports the autopilot purge query. Search filters (`WHERE deleted_at IS NULL`) do NOT need their own index — soft-deleted cardinality stays low and Postgres won't use the partial index for the negative predicate. Don't add a regular `(deleted_at)` index without measuring.
- Schema migration v34 (`destructive_guard_columns`) adds `pages.deleted_at` + the partial purge index; promotes `archived` from `sources.config` JSONB to real columns; backfills any pre-v0.26.5 JSONB shape.

Key commands added in v0.25.0:
- `gbrain eval export [--since DUR] [--limit N] [--tool query|search]` — stream captured `eval_candidates` rows as NDJSON to stdout. Every line starts with `"schema_version": 1` per the stable contract in `docs/eval-capture.md`. EPIPE-safe, progress heartbeats on stderr, deterministic ordering. Primary consumer is the sibling `gbrain-evals` repo for BrainBench-Real replay.
- `gbrain eval prune --older-than DUR [--dry-run]` — explicit retention cleanup for `eval_candidates`. Requires `--older-than` (never deletes without a window). Duration strings: 30d, 7d, 1h, 90m, 3600s.
- `gbrain eval replay --against FILE.ndjson [--limit N] [--top-regressions K] [--json] [--verbose]` — contributor-facing dev loop. Reads a captured NDJSON snapshot, re-runs each `query` / `search` op against the current brain, computes mean set-Jaccard@k between captured + current `retrieved_slugs`, top-1 stability rate, and latency Δ. JSON mode (`schema_version: 1`) for CI gating; human mode prints a regression table sorted worst-first. Closes the gap between "data captured" and "data used to gate a PR." See `docs/eval-bench.md` for the workflow.
- `gbrain eval cross-modal --task "..." --output <path> [--cycles N] [--slot-a-model ID] [--slot-b-model ID] [--slot-c-model ID] [--receipt-dir DIR] [--json]` (v0.27.x) — multi-model quality gate. Three different-provider frontier models score the OUTPUT against the TASK on 5 documented dimensions. Pass criterion: every dim mean >=7 AND no model scored any dim <5. Exit codes: 0 PASS, 1 FAIL, 2 INCONCLUSIVE (<2/3 models returned parseable scores). Default cycles=3 in TTY, **cycles=1 in non-TTY** (limits accidental scripted bulk spend). Default slots: `openai:gpt-4o` / `anthropic:claude-opus-4-7` / `google:gemini-1.5-pro` — refresh alongside model-family bumps. Receipts land at `~/.gbrain/.gbrain/eval-receipts/<slug>-<sha8-of-output>.json` (gbrainPath honors GBRAIN_HOME). Bypasses `connectEngine()` via the cli.ts no-DB branch — runs cleanly before `gbrain init`. Reuses `src/core/ai/gateway.ts:chat()` for config/auth (no parallel provider stack). Cost-estimate prints to stderr before each cycle (T11=B partial cost guardrail; full `--budget-usd N` is a follow-up TODO).
- `gbrain doctor` gains an `eval_capture` check: reads `eval_capture_failures` for the last 24h, groups by reason, warns when non-zero. Cross-process visibility (doctor runs in a separate process from MCP). Pre-v31 brains get `Skipped (table unavailable)` — non-fatal.
- Config addition: `eval: { capture?: boolean, scrub_pii?: boolean }` in `~/.gbrain/config.json`. **File-plane only** — `gbrain config set` writes the DB plane and does NOT control capture.
- **`GBRAIN_CONTRIBUTOR_MODE=1` env var** is the contributor-facing toggle. Capture is **off by default** as of v0.25.0; production users get a quiet brain. Resolution order: explicit `eval.capture` config wins both directions, then env var, then off. Documented in README.md, CONTRIBUTING.md, and `docs/eval-bench.md`.

Key commands added in v0.12.2:
- `gbrain repair-jsonb [--dry-run] [--json]` — repair double-encoded JSONB rows left over from v0.12.0-and-earlier Postgres writes. Idempotent; PGLite no-ops. The `v0_12_2` migration runs this automatically on `gbrain upgrade`.

Key commands added in v0.12.3:
- `gbrain orphans [--json] [--count] [--include-pseudo]` — surface pages with zero inbound wikilinks, grouped by domain. Auto-generated/raw/pseudo pages filtered by default. Also exposed as `find_orphans` MCP operation. The natural consumer of the v0.12.0 knowledge graph layer: once edges are captured, find the gaps.
- `gbrain doctor` gains two new reliability detection checks: `jsonb_integrity` (v0.12.0 Postgres double-encode damage) and `markdown_body_completeness` (pages truncated by the old splitBody bug). Detection only; fix hints point at `gbrain repair-jsonb` and `gbrain sync --force`.

Key commands added in v0.14.2:
- `gbrain sync --skip-failed` — acknowledge the current set of failed-parse files recorded in `~/.gbrain/sync-failures.jsonl` so the sync bookmark advances past them. Doctor's `sync_failures` check shows previously-skipped as "all acknowledged" instead of warning.
- `gbrain sync --retry-failed` — re-walk the unacknowledged failures and re-attempt parsing. If the files now succeed, they clear from the set and the bookmark advances naturally.
- `gbrain apply-migrations --force-retry <version>` — reset a wedged migration (3 consecutive partials with no completion) by appending a `'retry'` marker. Next `apply-migrations --yes` treats the version as fresh. `complete` status never regresses to `partial` either before or after a retry marker.
- `GBRAIN_POOL_SIZE` env var — honored by both the singleton pool (`src/core/db.ts`) and the parallel-import worker pool (`src/commands/import.ts`). Default is 10; lower to 2 for Supabase transaction pooler to avoid MaxClients crashes during `gbrain upgrade` subprocess spawns. Read at call time via `resolvePoolSize()`.
- `gbrain doctor` gains two new checks: `sync_failures` (surfaces unacknowledged parse failures with exact paths + fix hints) and `brain_score` (renders the 5-component breakdown when score < 100: embed coverage / 35, link density / 25, timeline coverage / 15, orphans / 15, dead links / 10 — sum equals total).

Key commands added in v0.26.0 (OAuth 2.1 + HTTP server + admin dashboard):
- `gbrain serve --http [--port 3131] [--token-ttl 3600] [--enable-dcr] [--log-full-params]` — HTTP MCP server with OAuth 2.1, admin dashboard at `/admin`, SSE activity feed at `/admin/events`, health check at `/health`. Prints admin bootstrap token on first start. Alongside (not replacing) stdio `gbrain serve`. As of v0.26.9, `mcp_request_log.params` and the SSE feed default to a redacted summary (`{redacted, kind, declared_keys, unknown_key_count, approx_bytes}`); pass `--log-full-params` to log raw payloads on a personal laptop with a startup warning.
- **OAuth client registration** — three paths:
  1. CLI: `gbrain auth register-client <name> --grant-types <types> --scopes <scopes>` (wired into `src/commands/auth.ts` as a thin wrapper over `GBrainOAuthProvider.registerClientManual`). Default grant types: `client_credentials`. Default scopes: `read`.
  2. Admin dashboard: Register client modal → credential reveal with Copy + Download JSON.
  3. SDK: `oauthProvider.registerClientManual(name, grantTypes, scopes, redirectUris)` for programmatic wrappers.
  `--enable-dcr` on `serve --http` opens the `/register` endpoint for RFC 7591 self-service registration (off by default).
- `gbrain auth create|list|revoke|test` — legacy bearer tokens still work and grandfather to `read+write+admin` scopes on the OAuth server. `auth` is wired as a first-class `gbrain` subcommand in v0.26.0 (previously only invokable via `bun run src/commands/auth.ts`). No migration required to keep pre-v0.26 clients working.

Key commands added in v0.14.3 (fix wave):
- `gbrain doctor --index-audit` — opt-in Postgres-only check reporting zero-scan indexes from `pg_stat_user_indexes`. Informational only; never auto-drops.
- `gbrain doctor` schema_version check fails loudly when `version=0` — catches `bun install -g github:...` postinstall failures (#218) and routes users to `gbrain apply-migrations --yes`.
- `gbrain jobs submit` gains `--max-stalled`, `--backoff-type`, `--backoff-delay`, `--backoff-jitter`, `--timeout-ms`, `--idempotency-key` — exposing existing `MinionJobInput` fields as first-class CLI flags.
- `gbrain jobs smoke --sigkill-rescue` — opt-in regression smoke case simulating a killed worker; asserts the v0.14.3 schema default (`max_stalled=5`) actually rescues on first stall.

Key commands added in v0.22.13 (PR #490):
- `gbrain sync --workers N` (alias `--concurrency N`) — parallelize the import phase using per-worker Postgres engines (small pool of 2 each) with an atomic queue index. Auto-concurrency: defaults to 4 workers when the diff exceeds 100 files. Smaller diffs stay serial. Explicit `--workers` always wins (even on a 30-file diff). PGLite forces serial regardless. Validation rejects `0`, negatives, non-integers loud (replaces the prior silent fall-through to auto-concurrency).
- `gbrain import --workers N` — same `parseWorkers()` validation as sync; same try/finally worker-engine cleanup. Behavior surface unchanged.

Key commands added in v0.22.16 (claw-test friction loop):
- `gbrain claw-test [--scenario fresh-install|upgrade-from-v0.18] [--keep-tempdir]` — scripted-mode CI gate that runs the full canonical first-day flow against a fresh tempdir. Asserts every expected `--progress-json` phase fired and doctor's `status === 'ok'`. ~30s, no API keys.
- `gbrain claw-test --live --agent openclaw` — friction-discovery mode. Spawns real openclaw, hands it `BRIEF.md`, captures stdin/stdout/stderr to `<run>/transcript.jsonl`, lets the agent log friction via the friction CLI. Run on demand; ~5–10 min and ~$1–2 in tokens.
- `gbrain claw-test --list-agents` — reports which agent runners are registered + their detection state (binary path or unavailable reason).
- `gbrain friction log --severity {confused|error|blocker|nit} --phase <name> --message <text> [--hint ...] [--kind {friction|delight}] [--run-id ...]` — append a friction or delight entry to the active run JSONL.
- `gbrain friction render --run-id <id> [--json] [--transcripts] [--no-redact]` — markdown report grouped by severity + phase; `--redact` is the default for md output (strips `$HOME`/`$CWD` placeholders so reports paste safely in PRs/issues).
- `gbrain friction list [--json]` — recent run-ids with friction/delight counts; interrupted runs marked `(interrupted)`.
- `gbrain friction summary --run-id <id> [--json]` — two-column friction + delight summary.
- `GBRAIN_HOME` env override is now honored uniformly across every gbrain write site (config, audit, friction, sync-failures, import checkpoint, integrity log, integrations heartbeat, migration rollback, etc.) — `gbrainPath(...)` from `src/core/config.ts` is the canonical helper. Read-side host-fingerprint detection (`~/.claude`/`~/.openclaw` etc.) intentionally NOT confined in v1; that's a v1.1 follow-up.

## Testing

### Test command tiers (v0.26.4 — parallel fast loop)

Five tiers of test commands, each with a clear scope:

| Command | What it runs | Wallclock | When to use |
|---|---|---|---|
| `bun run test` | Parallel unit-test fast loop. 8-shard fan-out via `scripts/run-unit-parallel.sh`, then a serial pass over `*.serial.test.ts`. Excludes `*.slow.test.ts` and `test/e2e/*`. No pre-checks, no typecheck. | ~85s on a Mac dev box (3650+ tests) | Inner edit loop. Default. |
| `bun run verify` | CI's authoritative pre-test gate set: `check:privacy && check:jsonb && check:progress && check:wasm && bun run typecheck`. The 4 checks `.github/workflows/test.yml` runs on shard 1 + typecheck. Single source of truth — CI literally calls `bun run verify`. | ~12s (wasm-compile dominates) | Before pushing; before `/ship`. |
| `bun run test:full` | `verify && bun run test && bun run test:slow && [smart e2e]`. The local equivalent of "everything CI runs." Smart e2e: runs e2e only when `DATABASE_URL` is set; else loud skip notice to stderr. | ~3-5min depending on slow + e2e | Pre-merge sanity, before opening a PR. |
| `bun run test:slow` | Just the `*.slow.test.ts` set (intentional cold-path correctness checks). | seconds-to-minutes | When touching slow-path code. |
| `bun run test:serial` | Just the `*.serial.test.ts` set (cross-file-contention quarantine; runs at `--max-concurrency=1`). | ~1s per quarantined file | Debugging a specific quarantined file. |
| `bun run test:e2e` | Real Postgres E2E. Requires Docker + `DATABASE_URL`. Sequential (template-DB parallelization is a v0.27+ TODO). | ~5-10min | Pre-ship; nightly. |
| `bun run check:all` | All 7 historical pre-checks (privacy + jsonb + progress + no-legacy-getconnection + trailing-newline + wasm + exports-count). Superset of `verify`. | ~10s | Local-only sweep. The 4 not in `verify` are nice-to-haves. |

### CI vs local: intentionally divergent file sets

- **CI matrix** (`.github/workflows/test.yml`) runs `scripts/test-shard.sh` 4-way, which uses FNV-1a hash bucketing and INCLUDES `*.slow.test.ts`. As of v0.31.4.1, CI EXCLUDES `*.serial.test.ts` from the hash buckets and runs them on shard 1 via `bun run test:serial` at `--max-concurrency=1`. Before that, serial files were hashed in alongside parallel files, which broke the `mock.module` quarantine (top-level mocks in serial files leaked into the parallel files they shared a shard process with — most visibly, `eval-takes-quality-runner.serial.test.ts` stubbed `gateway.ts` and broke every `gateway.embedMultimodal` test in `voyage-multimodal.test.ts` on shard 2). CI is the ground truth for "did everything pass."
- **Local fast loop** (`scripts/run-unit-shard.sh` via the parallel wrapper) uses round-robin-by-index sharding and EXCLUDES `*.slow.test.ts` AND `*.serial.test.ts`. Local trades coverage for inner-loop speed; CI catches what local skips.

This divergence is intentional. Don't try to make them equal — the two scripts deliberately solve different problems. The regression test at `test/scripts/run-unit-shard.test.ts` pins what the local fast loop should and shouldn't include.

### Failure-first logging

When `bun run test` finds any failure, the wrapper:

1. Writes failure blocks (each prefixed with `--- shard N: <test name> ---`) to `.context/test-failures.log` (workspace-local, gitignored). On systems without a writable `.context/`, falls back to `/tmp/gbrain-test-failures.log`.
2. Prints a loud stderr banner with the absolute log path, plus the last 30 lines of the failure log inlined. Banner survives `| head` / `| tail` / agent-side log truncation.
3. Writes a one-line-per-shard summary to `.context/test-summary.txt` (`shard N/M: pass=X fail=Y skip=Z rc=W`).
4. Exits non-zero. Empty failure log + non-zero exit = infrastructure problem (wedged shard, killed child); the banner says so.

If a shard wedges (per-shard `GBRAIN_TEST_SHARD_TIMEOUT` cap, default 600s), the wrapper writes `--- shard N: WEDGED after ${SHARD_TIMEOUT}s ---` to the failure log, includes the last 50 lines of the shard log, and proceeds with other shards' results.

### File taxonomy

- `*.test.ts` → fast loop (parallel 8-shard fan-out).
- `*.slow.test.ts` → run via `bun run test:slow` only (intentional cold-path tests; would dominate the fast loop's wallclock).
- `*.serial.test.ts` → run via `bun run test:serial` after the parallel pass completes; uses `--max-concurrency=1`. Quarantine for tests that share file-wide state and race when run alongside other files in the same `bun test` process. Currently: `test/brain-registry.serial.test.ts`, `test/reconcile-links.serial.test.ts`, `test/core/cycle.serial.test.ts`, `test/embed.serial.test.ts` (the latter two added in v0.26.7 — they use `mock.module(...)` which leaks across files in the shard process). **Do not put the parallelism back on a serial file unless you've fixed the contention root cause** (it just re-introduces the flake).
- `test/e2e/*.test.ts` → real-Postgres E2E. Skipped when `DATABASE_URL` is unset.
- `tests/heavy/*.sh` → ops-shape shell scripts. Cost minutes per run; NOT in default `bun test`. Run via `bun run test:heavy` or scheduled nightly via `.github/workflows/heavy-tests.yml`. Examples: pg_upgrade matrix (boot legacy brain → walk to head), RSS budget gate (measure peak worker RSS vs committed baseline), read-latency-under-sync (p50/p95/p99 under concurrent writer load), sync lock regression (N concurrent syncs assert 1 winner + N-1 lock-busy + zero leaked `gbrain_cycle_locks` rows). See `tests/heavy/README.md` for when to add a script here vs `*.slow.test.ts`. Files prefixed with `_` (e.g. `tests/heavy/_build_legacy_fixtures.sh`) are helpers/libs invoked by sibling tests — the runner skips them.
- `test/fuzz/*.test.ts` → property-based fuzz harness. Pure-validator targets in `pure-validators.test.ts` are guarded by `scripts/check-fuzz-purity.sh` (in `bun run verify`), which `bun build --target=bun` bundles each target and greps the resulting bundle for banned transitive imports (`node:fs`, `node:child_process`, engine modules). Anything that fails the guard moves to `mixed-validators.test.ts` (still property-tested, but no purity guarantee) or `filesystem-validators.test.ts` (fs-backed, uses temp dirs). Fuzz tests run in the default `bun test` loop because they're fast (~3s for ~12 properties × 1000 runs each).

The intra-file parallelism project (turn `bun test` into `bun test --concurrent` after sweeping shared-state contention sites) is sliced across v0.26.7 (foundation), v0.26.8 (env-mutation sweep), and v0.26.9 (PGLite sweep + codemod + measurement). v0.26.4 ships file-level parallelism only.

### Test-isolation lint and helpers (v0.26.7)

The cross-file flake class is enforced statically by `scripts/check-test-isolation.sh`, wired into `bun run verify` and `bun run check:all`. Rules (non-serial unit files only; `*.serial.test.ts` and `test/e2e/*` are skipped):

| Rule | What it bans | Fix |
|---|---|---|
| **R1** | `process.env.X = ...`, bracket assignment, `delete process.env.X`, `Object.assign(process.env, ...)`, `Reflect.set(process.env, ...)` | Use `withEnv()` from `test/helpers/with-env.ts`, OR rename file to `*.serial.test.ts` |
| **R2** | `mock.module(...)` anywhere in the file | Rename file to `*.serial.test.ts` (no DI on production code for testability) |
| **R3** | `new PGLiteEngine(` outside ~50 lines after a `beforeAll(` line | Use the canonical block (below) inside `beforeAll(` |
| **R4** | Files creating `new PGLiteEngine(` without `engine.disconnect(` inside an `afterAll(` block | Add `afterAll(() => engine.disconnect())` |

Files that violated these rules at the v0.26.7 baseline are listed in `scripts/check-test-isolation.allowlist`. **The allow-list MUST shrink over time** — never add new entries. v0.26.8 (env sweep) and v0.26.9 (PGLite sweep) remove entries as files get fixed.

#### Canonical PGLite block (R3 + R4 compliant)

Every test file that needs a PGLite engine should use this exact pattern:

```ts
import { PGLiteEngine } from '../src/core/pglite-engine.ts';
import { resetPgliteState } from './helpers/reset-pglite.ts';

let engine: PGLiteEngine;

beforeAll(async () => {
  engine = new PGLiteEngine();
  await engine.connect({});
  await engine.initSchema();
});

afterAll(async () => {
  await engine.disconnect();
});

beforeEach(async () => {
  await resetPgliteState(engine);
});
```

Why this exact shape: `beforeAll` creates a single engine per file (PGLite WASM cold-start + initSchema is ~20s); `beforeEach` truncates user data via `resetPgliteState` ("two orders of magnitude faster" than fresh-engine-per-test); `afterAll` disconnects so the engine doesn't leak across file boundaries within a shard process.

#### `withEnv` pattern (R1 fix)

```ts
import { withEnv } from './helpers/with-env.ts';

test('reads OPENAI_API_KEY', async () => {
  await withEnv({ OPENAI_API_KEY: 'sk-test' }, async () => {
    expect(loadConfig().openai_key).toBe('sk-test');
  });
});

// Delete a var (override is undefined):
await withEnv({ GBRAIN_HOME: undefined }, fn);

// Multiple keys:
await withEnv({ A: '1', B: '2', C: undefined }, fn);
```

`withEnv` saves the prior value of every key it touches and restores via try/finally — including when the callback throws. **It is cross-test safe but NOT intra-file concurrent-safe.** `process.env` is process-global; two `test.concurrent()` calls in the same file both touching the same key will race. Files using `withEnv` stay outside the future `test.concurrent()` codemod's eligibility filter.

#### When to quarantine instead of fix

Rename to `*.serial.test.ts` when:
- The file uses `mock.module(...)` (R2 — there's no clean fix without changing production code).
- The file is genuinely env-coupled (e.g. `gbrain-home-isolation.test.ts`, `claw-test-cli.test.ts`) — module-load env readers + ESM caching defeat dynamic-import-after-env tricks.
- The file's tests intentionally share state across `it()` boundaries.

Quarantine count cap: 10 (informational). Beyond that, push back on the design.

### Inventory (legacy)

`bun test` runs all tests. After the v0.12.1 release: ~75 unit test files + 8 E2E test files (1412 unit pass, 119 E2E when `DATABASE_URL` is set — skip gracefully otherwise). Unit tests run
without a database. E2E tests skip gracefully when `DATABASE_URL` is not set.

Unit tests: `test/markdown.test.ts` (frontmatter parsing), `test/chunkers/recursive.test.ts`
(chunking), `test/parity.test.ts` (operations contract
parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redaction),
`test/files.test.ts` (MIME/hash), `test/import-file.test.ts` (import pipeline),
`test/upgrade.test.ts` (schema migrations),
`test/file-migration.test.ts` (file migration), `test/file-resolver.test.ts` (file resolution),
`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix + v0.13.1 assertions on v12/v13 SQL shape, `sqlFor` + `transaction:false` runner semantics, the `max_stalled DEFAULT 1` regression guard, and v0.22.6.1 v24 `sqlFor.pglite: ''` no-op assertion),
`test/bootstrap.test.ts` (v0.22.6.1 — bootstrap contract: no-op on fresh install, idempotent across two `initSchema()` calls, no-op on modern brain that already has every probed column, full bootstrap path on simulated pre-v0.18 brain, fresh-install regression guard, pre-v0.13 `links` shape coverage),
`test/schema-bootstrap-coverage.test.ts` (v0.22.6.1 CI guard — `REQUIRED_BOOTSTRAP_COVERAGE` lists every forward reference in PGLITE_SCHEMA_SQL; the test fails loudly if `applyForwardReferenceBootstrap` skips one. When you add a column-with-index to the embedded schema blob, you extend both arrays or this guard fails. The pattern that broke gbrain ten times in two years is now structurally prevented. **v0.35.5.0:** test now also parses `src/core/migrate.ts` source text for every `ALTER TABLE ... ADD COLUMN` (top-level `sql:`, `sqlFor.{postgres,pglite}` overrides, AND handler-body `engine.runMigration(N, \`ALTER TABLE ...\`)`), and asserts each (table, column) pair is covered by the bootstrap OR by the schema blob's CREATE TABLE bodies. Catches the column-only forward-reference class (e.g. `sources.archived` shape from v0.26.5, `oauth_clients.source_id` from v0.34.1) that the pre-existing CREATE INDEX parser couldn't see. Pre-existing parser bug fixed in same wave: `parseBaseTableColumns` now strips SQL line + block comments before identifying column names so commented-out lines no longer hide adjacent columns from coverage.),
`test/helpers/schema-diff.ts` + `test/helpers/schema-diff.test.ts` + `test/e2e/schema-drift.test.ts` (v0.26.6 #588 — cross-engine schema parity gate. Helper exports pure `snapshotSchema(query)` / `diffSnapshots(pg, pglite, opts)` / `formatDiffForFailure(diff)` / `isCleanDiff(diff)` over a four-tuple per column (`data_type`, `udt_name`, `is_nullable`, `column_default`). E2E test spins up fresh PGLite + Postgres, runs `engine.initSchema()` on each (bootstrap + schema replay + migrations), snapshots `information_schema.columns`, then diffs. 2-table allowlist (`files`, `file_migration_ledger`) — every other Postgres table must reach PGLite via PGLITE_SCHEMA_SQL or a migration's `sqlFor.pglite` branch. Sentinels for `oauth_clients`, `mcp_request_log`, `access_tokens`, `eval_candidates` give tighter blame messages. Skip-gracefully without `DATABASE_URL`. Wired into `scripts/e2e-test-map.ts` so changes to `src/schema.sql`, `src/core/pglite-schema.ts`, or `src/core/migrate.ts` trigger it. The failure message names every drift with a paste-ready hint pointing at `src/core/pglite-schema.ts`.),
`test/setup-branching.test.ts` (setup flow), `test/slug-validation.test.ts` (slug validation),
`test/storage.test.ts` (storage backends), `test/supabase-admin.test.ts` (Supabase admin),
`test/yaml-lite.test.ts` (YAML parsing), `test/check-update.test.ts` (version check + update CLI),
`test/pglite-engine.test.ts` (PGLite engine, all 40 BrainEngine methods including 11 cases for `addLinksBatch` / `addTimelineEntriesBatch`: empty batch, missing optionals, within-batch dedup via ON CONFLICT, missing-slug rows dropped by JOIN, half-existing batch, batch of 100 + v0.13.1 `connect()` error-wrap assertion (original error nested, #223 link in message, lock released)),
`test/engine-factory.test.ts` (engine factory + dynamic imports),
`test/integrations.test.ts` (recipe parsing, CLI routing, recipe validation),
`test/publish.test.ts` (content stripping, encryption, password generation, HTML output),
`test/backlinks.test.ts` (entity extraction, back-link detection, timeline entry generation),
`test/lint.test.ts` (LLM artifact detection, code fence stripping, frontmatter validation),
`test/report.test.ts` (report format, directory structure),
`test/skills-conformance.test.ts` (skill frontmatter + required sections validation),
`test/resolver.test.ts` (RESOLVER.md coverage, routing validation + v0.20.4 round-trip: every quoted RESOLVER.md trigger must match a frontmatter `triggers:` entry in the target skill, and every `name="<word>"` reference in any SKILL.md must resolve to a declared op in `src/core/operations.ts` or a Minions handler in `PROTECTED_JOB_NAMES`),
`test/search.test.ts` (RRF normalization, compiled truth boost, cosine similarity, dedup key),
`test/sql-ranking.test.ts` (v0.22.0 source-boost helpers: 39 cases covering longest-prefix-match in SQL CASE, detail=high temporal-bypass, three-meta-char LIKE escape (%, _, \\), single-quote SQL-literal doubling, env override parsing for GBRAIN_SOURCE_BOOST + GBRAIN_SEARCH_EXCLUDE, resolveBoostMap / resolveHardExcludes merge semantics),
`test/dedup.test.ts` (source-aware dedup, compiled truth guarantee, layer interactions),
`test/intent.test.ts` (query intent classification: entity/temporal/event/general),
`test/eval.test.ts` (retrieval metrics: precisionAtK, recallAtK, mrr, ndcgAtK, parseQrels),
`test/check-resolvable.test.ts` (resolver reachability, MECE overlap, gap detection, DRY checks + v0.14.1 proximity-based DRY detection + `extractDelegationTargets` coverage — 13 DRY cases),
`test/dry-fix.test.ts` (v0.14.1 auto-fix: three shape-aware expander pure-function tests, five guards — working-tree-dirty, no-git-backup, inside-code-fence, already-delegated within 40 lines, ambiguous-multi-match, block-is-callout — 28 cases),
`test/doctor-fix.test.ts` (v0.14.1 `gbrain doctor --fix` CLI integration: dry-run preview, apply path, JSON output shape — 3 cases),
`test/backoff.test.ts` (load-aware throttling, concurrency limits, active hours),
`test/fail-improve.test.ts` (deterministic/LLM cascade, JSONL logging, test generation, rotation),
`test/transcription.test.ts` (provider detection, format validation, API key errors),
`test/enrichment-service.test.ts` (entity slugification, extraction, tier escalation),
`test/data-research.test.ts` (recipe validation, MRR/ARR extraction, dedup, tracker parsing, HTML stripping),
`test/minions.test.ts` (Minions job queue v7: CRUD, state machine, backoff, stall detection, dependencies, worker lifecycle, lock management, claim mechanics, depth/child-cap, timeouts, cascade kill, idempotency, child_done inbox, attachments, removeOnComplete/Fail + v0.13.1 `max_stalled` clamp/default/plumbing coverage),
`test/extract.test.ts` (link extraction, timeline extraction, frontmatter parsing, directory type inference),
`test/extract-db.test.ts` (gbrain extract --source db: typed link inference, idempotency, --type filter, --dry-run JSON output),
`test/extract-fs.test.ts` (gbrain extract --source fs: first-run inserts + second-run reports zero, dry-run dedups candidates across files, second-run perf regression guard — the v0.12.1 N+1 dedup bug),
`test/link-extraction.test.ts` (canonical extractEntityRefs both formats, extractPageLinks dedup, inferLinkType heuristics, parseTimelineEntries date variants, isAutoLinkEnabled config),
`test/graph-query.test.ts` (direction in/out/both, type filter, indented tree output),
`test/features.test.ts` (feature scanning, brain_score calculation, CLI routing, persistence),
`test/file-upload-security.test.ts` (symlink traversal, cwd confinement, slug + filename allowlists, remote vs local trust),
`test/query-sanitization.test.ts` (prompt-injection stripping, output sanitization, structural boundary),
`test/search-limit.test.ts` (clampSearchLimit default/cap behavior across list_pages and get_ingest_log),
`test/repair-jsonb.test.ts` (v0.12.2 JSONB repair: TARGETS list, idempotency, engine-awareness),
`test/migrations-v0_12_2.test.ts` (v0.12.2 orchestrator phases: schema → repair → verify → record),
`test/markdown.test.ts` (splitBody sentinel precedence, horizontal-rule preservation, inferType wiki subtypes),
`test/orphans.test.ts` (v0.12.3 orphans command: detection, pseudo filtering, text/json/count outputs, MCP op),
`test/postgres-engine.test.ts` (v0.12.3 statement_timeout scoping: `sql.begin` + `SET LOCAL` shape, source-level grep guardrail against reintroduced bare `SET statement_timeout`),
`test/sync.test.ts` (sync logic + v0.12.3 regression guard asserting top-level `engine.transaction` is not called),
`test/sync-concurrency.test.ts` (v0.22.13 PR #490: 17 cases covering `autoConcurrency()` thresholds + PGLite-forces-serial + explicit-override clamping, `shouldRunParallel()` Q1 explicit-bypasses-floor contract, and `parseWorkers()` validation that rejects `'0'`/`'-3'`/`'foo'`/`'1.5'`/trailing chars),
`test/sync-parallel.test.ts` (v0.22.13 PR #490: PGLite-routed coverage of the bookmark gate under concurrency request, head-drift gate, vanished-file failure capture, PGLite-stays-serial, and the `gbrain-sync` writer-lock contract — 7 cases),
`test/sync-failures.test.ts` (v0.22.12: 28 cases pinning `classifyErrorCode` regex coverage for all 12 codes against literal production message strings from `markdown.ts:159-244` and `import-file.ts:199, 347, 352, 401`; `summarizeFailuresByCode` sort + pre-classified-honor; `recordSyncFailures` code-field persistence; `acknowledgeSyncFailures` AcknowledgeResult shape + backfill on pre-v0.22.12 entries),
`test/doctor.test.ts` (doctor command + v0.12.3 assertions that `jsonb_integrity` scans the four v0.12.0 write sites and `markdown_body_completeness` is present),
`test/utils.test.ts` (shared SQL utilities + `tryParseEmbedding` null-return and single-warn semantics),
`test/build-llms.test.ts` (llms.txt/llms-full.txt generator: path resolution, idempotence, spec shape, regen-drift guard, content contract, AGENTS.md install-path mirror, size-budget enforcement — 7 cases),
`test/oauth.test.ts` (v0.26.0 OAuth 2.1 provider — 27 cases: register, getClient, `client_credentials` grant exchange, `authorization_code` flow with PKCE challenge / verifier, refresh token rotation, `verifyAccessToken` with both OAuth + legacy `access_tokens` fallback, `revokeToken`, `sweepExpiredTokens`, and a contract test asserting `scope` + `localOnly` annotations are set correctly on all 30 operations; **v0.26.2** adds 5 `coerceTimestamp` unit cases (null/undefined/string/number/throw-on-NaN), NULL-`expires_at`-as-expired contract tests for both refresh + access token paths, and a cascade-delete contract test asserting `revoke-client` purges `oauth_tokens` + `oauth_codes` rows via FK CASCADE; **v0.26.9** adds 14 cases pinning the F1/F2/F3/F4/F5/F6/F7c/F12 invariants, including the F1/F4 cross-client isolation pattern (wrong-client attempt MUST reject AND rightful owner MUST still succeed atomically afterward) and the empty-string `redirect_uri` bypass guard surfaced during adversarial review),
`test/mcp-dispatch-summarize.test.ts` (v0.26.9 — 7 cases pinning F8 `summarizeMcpParams` invariants: declared-keys allow-list intersection, attacker-key-name leak guard (unknown keys counted not named), 1KB byte bucketing for size-probe defense, missing op falls through to fully-redacted shape, declared-keys sorted for deterministic output),
`test/trust-boundary-contract.test.ts` (v0.26.9 — 4 cases pinning F7b fail-closed semantics under cast bypass: `ctx.remote === undefined` treated as remote/untrusted at every flipped call site, `as any` and `Partial<>` spreads can't downgrade trust by accident),
`test/check-resolvable-cli.test.ts` (v0.19 CLI wrapper: exit codes, JSON envelope shape, AGENTS.md fallback chain),
`test/regression-v0_16_4.test.ts` (findRepoRoot regression guard — hermetic startDir parameterization),
`test/repo-root.test.ts` (v0.16.4 / v0.19 / v0.31.7 — 20 cases: `findRepoRoot` walk semantics + default-arg parity, the 4-tier `autoDetectSkillsDir` fallback chain (`$OPENCLAW_WORKSPACE` → `~/.openclaw/workspace` → repo-root → `./skills`), W1 RESOLVER.md/AGENTS.md filename precedence, D-CX-4 explicit-env-wins-over-repo-root, and 8 new v0.31.7 D3+D5 cases pinning tier-0 `$GBRAIN_SKILLS_DIR` valid/invalid/precedence-over-OPENCLAW_WORKSPACE, the install-path walk in `autoDetectSkillsDirReadOnly`, no-drift on primary success, `AUTO_DETECT_HINT` + `AUTO_DETECT_HINT_READ_ONLY` content, and the D5 regression guard asserting the shared `autoDetectSkillsDir` MUST NEVER return `'install_path'` source — that's how the read-path/write-path split stays safe),
`test/resolver-merge.test.ts` (v0.31.7 — 8 cases pinning the multi-file resolver merge: `findAllResolverFiles` empty / RESOLVER.md-only / AGENTS.md-only / both-present (RESOLVER.md first), and `checkResolvable` merge semantics across `skills/RESOLVER.md` + `../AGENTS.md` for the OpenClaw layout where the skillpack ships a thin RESOLVER.md and the real dispatcher lives at the workspace root — dedup by `skillPath` (first occurrence wins), AGENTS.md-at-workspace-root works alone, and the previously-unreachable 187/224 OpenClaw skills become reachable),
`test/filing-audit.test.ts` (v0.19 Check 6: `writes_pages` / `writes_to` frontmatter, filing-rules JSON validation),
`test/skill-brain-first.test.ts` (v0.37.1.0 — 56 cases: shared frontmatter parser, `analyzeSkillBrainFirst` compliance ladder across 9 fixtures under `test/fixtures/brain-first-skills/` (compliant-callout, compliant-phase, compliant-position, exempt-frontmatter, missing-brain-first, multi-pattern, negation-prose, no-external, typo-frontmatter), offset helpers, external-lookup regex shape, audit snapshot+diff transition logic, PR #1206 `FORMERLY_HARDCODED_EXEMPT` regression absorption),
`test/e2e/skill-brain-first.test.ts` (v0.37.1.0 — 12 E2E cases: doctor reports `skill_brain_first` check with structured issues; `--fix --dry-run` previews insertion without writing; `--fix` applies the canonical Convention callout idempotently; `brain_first: exempt` frontmatter resolves the warn; `brain_first_typo` surfaces paste-ready hint; audit JSONL records `detected` / `resolved` / `fixed` transitions; stable brain emits 0 audit lines/run),
`test/routing-eval.test.ts` (v0.19 Check 5: fixture parsing, structural routing, ambiguous_with, Haiku tie-break layer),
`test/skill-manifest.test.ts` (v0.19 skill manifest parser: drift detection, managed-block markers),
`test/skillify-scaffold.test.ts` (v0.19 `gbrain skillify scaffold` stubs: SKILL.md, script, tests, routing-eval fixtures),
`test/skillpack-install.test.ts` (v0.19 `gbrain skillpack install` managed-block install / update / no-clobber semantics),
`test/skillpack-sync-guard.test.ts` (v0.19 sync-guard: bundled skills stay byte-identical to `skills/` source),
`test/http-transport.test.ts` (v0.22.7 HTTP transport: 23 unit cases covering bearer auth + missing/no-Bearer/unknown/revoked + `/health` bypass, F1+F2 round-trip via dispatch.ts, F3 invalid_params, application/json response shape (not SSE), CORS default-deny + allowlist, body cap on Content-Length AND chunked, two-bucket rate limit (refill, exhaust+Retry-After, LRU eviction, TTL prune, pre-auth IP fires before DB), and `mcp_request_log` audit on success + auth_failed),
`test/restart-sweep.test.ts` (v0.28.3 — 27 bun:test cases for the `recipes/restart-sweep.md` inlined script: sentinel-anchored fenced-block extraction with salted tmp filenames to bypass ESM cache; constructor-time env reads (proves no module-load snapshot); idempotency layer load/save/atomic-tmp-rename/corrupt-JSON-recovery/30-day-prune; `(sessionKey, lastAlertedAt)` cooldown gate with 6h threshold (the C1 fix that survives synthesized restartTime); AGGRESSIVE-gate two-state tests; execFile argv shape proving shell metachars in `OPENCLAW_TELEGRAM_GROUP` cannot reach `/bin/sh`; real-`\n`-not-literal alert formatting; `GBRAIN_HOME` state path override),
`test/eval-longmemeval.test.ts` (v0.28.8 LongMemEval harness — 12 hermetic cases with no `DATABASE_URL` and no API keys: PGLite create + reset over runtime-enumerated `pg_tables`, infrastructure-table preservation across resets, JSONL question parsing, retrieval-only and answer-gen modes via stubbed `ThinkLLMClient`, `--limit` cutoff, `--keyword-only` vs hybrid, default `--expansion=off` behavior, perf gate (p50 < 30ms / p99 < 50ms warm reset+import+search on Apple Silicon), `--help` works without a configured brain, fixture round-trip via `test/fixtures/longmemeval-mini.jsonl`),
`test/longmemeval-sanitize.test.ts` (v0.28.8 sanitization parity: 12 cases pinning that `INJECTION_PATTERNS` from `src/core/think/sanitize.ts` is the single source of truth — adding a pattern there must cover both `<take>` framing and `<chat_session>` framing, no per-surface regex drift).

E2E tests (`test/e2e/`): Run against real Postgres+pgvector. Require `DATABASE_URL`.
- `bun run test:e2e` runs Tier 1 (mechanical, all operations, no API keys). Includes 9 dedicated cases for the postgres-engine `addLinksBatch` / `addTimelineEntriesBatch` bind path — postgres-js's `unnest()` binding is structurally different from PGLite's and gets its own coverage.
- `test/e2e/search-quality.test.ts` runs search quality E2E against PGLite (no API keys, in-memory)
- `test/e2e/graph-quality.test.ts` runs the v0.10.3 knowledge graph pipeline (auto-link via put_page, reconciliation, traversePaths) against PGLite in-memory
- `test/e2e/postgres-jsonb.test.ts` — v0.12.2 regression test. Round-trips all 5 JSONB write sites (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter) against real Postgres and asserts `jsonb_typeof='object'` plus `->>'key'` returns the expected scalar. The test that should have caught the original double-encode bug.
- `test/e2e/integrity-batch.test.ts` (v0.22.8) — parity tests for `scanIntegrity`'s batch-load fast path vs sequential. Four cases (dedup, hits, validate, topPages) seed a fixture and assert both paths return identical results. Dedup case uses raw SQL via `getConn().unsafe()` to seed a `(test-source-2, people/alice)` row alongside the default-source row, since `engine.putPage` doesn't take a `source_id`. Pins the codex-caught multi-source overcounting regression.
- `test/e2e/jsonb-roundtrip.test.ts` — v0.12.3 companion regression against the 4 doctor-scanned JSONB sites. Assertion-level overlap with `postgres-jsonb.test.ts` is intentional defense-in-depth: if doctor's scan surface ever drifts from the actual write surface, one of these tests catches it.
- `test/e2e/sync.test.ts` (v0.22.12 — `--skip-failed` failure-loop test, alongside the existing 13 happy-path tests): exercises the full chain — broken file → `performSync` returns `blocked_by_failures` with grouped breakdown → `performSync({skipFailed: true})` advances bookmark and returns `AcknowledgeResult` with code summary → second broken file → second cycle. Saves and restores the user's real `~/.gbrain/sync-failures.jsonl` so the test is hermetic on a developer machine. Asserts bookmark gating, JSONL state, dedup across paths, summary aggregation, and the literal doctor-rendering string format. This is the integration test that proves the v0.22.12 chain holds together — unit tests cover the pure functions in isolation, this covers the integration.
- `test/e2e/upgrade.test.ts` runs check-update E2E against real GitHub API (network required)
- `test/e2e/minions-shell-pglite.test.ts` (v0.20.4) exercises the PGLite `--follow` inline shell-job path (in-memory, no `DATABASE_URL` required) — the path the consolidated minion-orchestrator skill documents for dev use
- `test/e2e/openclaw-reference-compat.test.ts` (v0.19) — exercises `check-resolvable` + `skillpack install` against a minimal AGENTS.md workspace fixture (`test/fixtures/openclaw-reference-minimal/`), regression guard for the 107-skill OpenClaw deployment shape
- `test/e2e/search-swamp.test.ts` (v0.22.0) — reproduces the headline source-swamp case. Seeds a curated `originals/talks/article-outline-fat-code` page against two `wintermute/chat/` pages stuffed with the same multi-word phrase. Asserts the article wins keyword AND vector ranking, that `detail=high` lets the chat swamp re-surface (temporal-query workflow preserved), and that `source_id` passes through the two-stage CTE intact. PGLite in-memory.
- `test/e2e/search-exclude.test.ts` (v0.22.0) — verifies `test/` + `archive/` pages are hidden by default, that `include_slug_prefixes` opts back in, and that caller-supplied `exclude_slug_prefixes` adds to defaults. Both keyword and vector search paths covered.
- `test/e2e/engine-parity.test.ts` (v0.22.0) — Postgres ↔ PGLite top-result and result-set parity for `searchKeyword` + `searchVector`. Codex flagged that Postgres ranks pages then picks best chunk while PGLite returns chunks directly — without parity coverage the source-boost fix could pass on PGLite and fail on Postgres. Skips gracefully when `DATABASE_URL` is unset.
- `test/e2e/postgres-bootstrap.test.ts` (v0.22.6.1) — exercises `PostgresEngine.initSchema()` directly against a fresh real Postgres database. Asserts the bootstrap path is no-op on fresh installs and that SCHEMA_SQL replays cleanly through the engine path (not via the standalone `db.initSchema` from `src/core/db.ts`, which would have produced false-positive coverage). Codex caught the E2E-shape gap during plan review.
- `test/e2e/http-transport.test.ts` (v0.22.7) — 8 cases against real Postgres covering `gbrain serve --http` end-to-end: bearer auth round-trip, `last_used_at` SQL-level debounce semantics, `mcp_request_log` row insertion on success and auth_failed paths, `/health` DB-down → 503 (DB-probing health check), and the F1+F2+F3 dispatch round-trip with a real operation. Skips gracefully when `DATABASE_URL` is unset.
- `test/e2e/serve-http-oauth.test.ts` (v0.26.0, expanded v0.26.2, expanded v0.26.9) — real-Postgres E2E against `gbrain serve --http` with full OAuth 2.1. Spawns a subprocess server, registers a client via the CLI, mints `client_credentials` tokens, exercises the `/mcp` JSON-RPC pipeline. **v0.26.2 adds:** real DCR `/register` HTTP-level response-shape test (asserts `typeof body.client_id_issued_at === 'number'` over the wire — RFC 7591 §3.2.1 spec compliance, not just internal-store shape); real CLI subprocess test for `revoke-client` (registers → mints token → revokes via `execSync` → asserts token rejected at `/mcp` → asserts re-run exits 1); server fixture flips on `--enable-dcr` so `/register` is reachable. **bun execSync env-inheritance fix:** bun's `execSync` does NOT inherit env mutations done via `process.env.X = ...`, only OS-level env from before bun started. helpers.ts loads `.env.testing` and sets `DATABASE_URL` via `process.env` mutation, which is invisible to subprocesses unless `env: { ...process.env }` is passed explicitly — every subprocess call in this file passes `env: { ...process.env }` for that reason. Reference fix for the next maintainer hitting the same failure mode in sibling sync/cycle/dream/claw-test E2Es. `afterAll` cleanup is guarded on `clientId` (won't throw if `beforeAll` failed before registration); cleanup errors surface to stderr without throwing so real test failures aren't masked. Tracks DCR-registered clients alongside the manual one. **v0.26.9** adds 2 regressions for the F7 trust-boundary fix: an HTTP MCP `submit_job` for `name: "shell"` MUST reject with a permission error (proving the request handler now sets `remote: true` and `submit_job`'s protected-name guard fires), and the same guard rejects subagent submission. Closes the OAuth-token-to-RCE escalation path. Skips gracefully when `DATABASE_URL` is unset.
- `test/e2e/sync-parallel.test.ts` (v0.22.13 PR #490) — DATABASE_URL-gated. T2: 60-file Postgres sync at concurrency=4 imports all + no connection leak (probes `pg_stat_activity` before/after to confirm worker engines disconnected). P4: 120-file serial-vs-parallel benchmark prints `SYNC_PARALLEL_BENCH N files | serial=Xms | parallel(4)=Yms | speedup=Zx` for CHANGELOG quoting. Asserts parallel ≤ serial × 1.5 (CI-noise tolerant; not a strict speedup gate).
- `test/e2e/multi-source-bug-class.test.ts` (v0.32.8, PR #860) — 7-case PGLite in-memory regression suite pinning every bug site fixed in this PR: `listAllPageRefs` ordering by `(source_id, slug)` (F11), `getPage` with sourceId picks the right `(source, slug)` row (F2), `extract-takes` processes both overlapping `people/alice` rows independently, `listPages` filters correctly with `PageFilters.sourceId`, `addLinksBatch` with `from/to_source_id` targets the right rows (F4), `validateSourceId` rejects path traversal (F6), reverse-write disk layout uses `brainDir/.sources/<id>/<slug>.md` for non-default sources (F6). No DATABASE_URL needed. Wired into `scripts/e2e-test-map.ts` so changes to extract-takes / patterns / synthesize / embed / extract / migrate-engine auto-trigger this test. Companion: `test/e2e/integrity-batch.test.ts`'s "multi-source duplicate slugs scan once" case was pinning the pre-fix bug — assertion flipped in v0.32.8 to expect both batch + sequential paths report 2.
- `test/e2e/source-isolation-pglite.test.ts` (v0.34.1.0, #861) — 14-case PGLite in-memory regression suite pinning the source-isolation P0 seal at two layers. Engine layer: `searchKeyword` / `searchVector` / `searchKeywordChunks` / `listPages` / `getPage` / `traverseGraph` / `traversePaths` apply `sourceId` (scalar fast path) and `sourceIds` (array path) correctly across both engines. Op-handler layer: routes through `sourceScopeOpts(ctx)` so a `read+write`-scoped OAuth client bound to `--source dept-x` cannot see rows from neighboring sources via `search`, `query`, `list_pages`, `get_page`, or `find_experts`. Covers both `ctx.sourceId` (single-source clients) and `ctx.auth.allowedSources` (federated_read clients) precedence; federated array wins over scalar wins over nothing. No DATABASE_URL needed.
- `test/openai-compat-multimodal.test.ts` (v0.34.1.0, #875) — 11-case unit suite for the gateway's openai-compatible multimodal path: happy-path single + multi-input embedding, unauthenticated proxy mode, dimension-mismatch guard (D12; throws `AIConfigError` with model id + observed + expected pre-storage), default-dim fallback when recipe declares `default_dims`, HTTP 401 / 400 / malformed-JSON / non-array error paths, plus a regression test that the existing Voyage `/multimodalembeddings` recipe still routes through its dedicated path (not the openai-compatible one). Hermetic via the `__setEmbedTransportForTests` seam.
- `test/serve-stdio-lifecycle.test.ts` (extended v0.34.1.0, #870) — adds 3 new cases for the `MCP_STDIO=1` env guard: stdin EOF does NOT trigger shutdown when the env is set, SIGTERM still does (guard scope is correct), unset env preserves the pre-v0.34 CLI lifecycle. Exercises the `ServeOptions.mcpStdio?: boolean` test seam directly so tests don't mutate `process.env`.
- `test/oauth.test.ts` (extended v0.34.1.0, #909) — 5 new cases for the PKCE DCR public-client gate: `registerClient` with `token_endpoint_auth_method: "none"` returns no `client_secret` field on the public client, default `client_secret_post` clients still get the one-time-reveal secret, `getClient` NULL→undefined normalization so the SDK's clientAuth path accepts public clients, full PKCE `/authorize` → `/token` round-trip against a public client (no client_secret presented), and a regression test that the public-vs-confidential branch doesn't break confidential client `client_secret_post` exchange.
- Tier 2 (`skills.test.ts`) requires OpenClaw + API keys, runs nightly in CI
- If `.env.testing` doesn't exist in this directory, check sibling worktrees for one:
  `find ../  -maxdepth 2 -name .env.testing -print -quit` and copy it here if found.
- **Run E2E tests without asking permission.** When you want to verify behavior,
  there's a relevant E2E test, or you're shipping touching anything covered by an
  E2E suite — just spin up the test DB, run the tests, and tear down. Don't ask,
  don't propose it, don't defer. The lifecycle is short (~2-30s startup, sub-minute
  tests, instant teardown) and the gate value is high. Skipping with "DATABASE_URL
  unset" is silent regression, not caution.

### API keys and running ALL tests

ALWAYS source the user's shell profile before running tests:

```bash
source ~/.zshrc 2>/dev/null || true
```

This loads `OPENAI_API_KEY` and `ANTHROPIC_API_KEY`. Without these, Tier 2 tests
skip silently. Do NOT skip Tier 2 tests just because they require API keys — load
the keys and run them.

When asked to "run all E2E tests" or "run tests", that means ALL tiers:
- Tier 1: `bun run test:e2e` (mechanical, sync, upgrade — no API keys needed)
- Tier 2: `test/e2e/skills.test.ts` (requires OpenAI + Anthropic + openclaw CLI)
- Always spin up the test DB, source zshrc, run everything, tear down.

### E2E test DB lifecycle (ALWAYS follow this)

You are responsible for spinning up and tearing down the test Postgres container.
Do not leave containers running after tests. Do not skip E2E tests, do not ask
permission to run them — see the "run without asking" rule above.

1. **Check for `.env.testing`** — if missing, copy from sibling worktree.
   Read it to get the DATABASE_URL (it has the port number).
2. **Check if the port is free:**
   `docker ps --filter "publish=PORT"` — if another container is on that port,
   pick a different port (try 5435, 5436, 5437) and start on that one instead.
3. **Start the test DB:**
   ```bash
   docker run -d --name gbrain-test-pg \
     -e POSTGRES_USER=postgres -e POSTGRES_PASSWORD=postgres \
     -e POSTGRES_DB=gbrain_test \
     -p PORT:5432 pgvector/pgvector:pg16
   ```
   Wait for ready: `docker exec gbrain-test-pg pg_isready -U postgres`
4. **Bootstrap the schema** (required — fresh containers have no `oauth_clients`,
   `mcp_request_log`, `pages` etc.; tests like `serve-http-oauth.test.ts` will fail
   with `relation "oauth_clients" does not exist` if you skip this):
   ```bash
   DATABASE_URL=postgresql://postgres:postgres@localhost:PORT/gbrain_test \
     bun run src/cli.ts doctor --json > /dev/null 2>&1
   ```
   `gbrain doctor` triggers `initSchema()` on first connect, which is the canonical
   way to bring a fresh DB to head. `apply-migrations --yes` alone does NOT seed
   the base schema — it runs ALTER-style migrations on top of `initSchema`. Tests
   that bypass the engine (raw `execSync`-spawned `auth register-client`) hit the
   schema directly and need this step to have run first.
5. **Run E2E tests:**
   `DATABASE_URL=postgresql://postgres:postgres@localhost:PORT/gbrain_test bun run test:e2e`
6. **Tear down immediately after tests finish (pass or fail):**
   `docker stop gbrain-test-pg && docker rm gbrain-test-pg`

Never leave `gbrain-test-pg` running. If you find a stale one from a previous run,
stop and remove it before starting a new one.

## Search Mode (v0.32.3)

GBrain ships three named search modes that bundle the search-lite knobs from
PR #897 into a single config key. Pick one at install time; the rest of the
project resolves through `src/core/search/mode.ts`.

| Knob                          | `conservative` | `balanced` | `tokenmax`     |
|-------------------------------|----------------|------------|----------------|
| `cache.enabled`               | true           | true       | true           |
| `cache.similarity_threshold`  | 0.92           | 0.92       | 0.92           |
| `cache.ttl_seconds`           | 3600           | 3600       | 3600           |
| `intentWeighting`             | true           | true       | true           |
| `tokenBudget`                 | **4000**       | **12000**  | **off**        |
| `expansion` (LLM multi-query) | false          | false      | **true**       |
| `searchLimit` default         | 10             | 25         | 50             |

**Cost anchors (downstream agent input cost — gbrain itself is rounding error).**
The corner-to-corner spread is 25x once you pair mode with downstream model.
Chunks ~400 tokens avg. Per-query cost @ 10K queries/month (typical
single-user volume), full search payload, no cache savings:

| Mode \ Downstream | Haiku 4.5 (\$1/M) | Sonnet 4.6 (\$3/M) | Opus 4.7 (\$5/M) |
|---|---|---|---|
| conservative (~4K) | **\$40/mo** | \$120/mo | \$200/mo |
| balanced (~10K) | \$100/mo | \$300/mo | \$500/mo |
| tokenmax (~20K) | \$200/mo | \$600/mo | **\$1,000/mo** |

Scales linearly: multiply by 10 for 100K/mo (heavy power user / multi-user
fleet); divide by 10 for 1K/mo (light usage). Natural pairings span ~4x.
Mismatches (tokenmax+Haiku, conservative+Opus) waste capacity differently
— too-big payload overwhelms a cheap model; too-small payload starves an
expensive one.

tokenmax adds ~\$1.50 per 1K queries in Haiku expansion calls on top of
the matrix (\$15/mo @ 10K). Cache hits cut all numbers ~50%. **The cost
picker copy in `gbrain init` carries the same matrix verbatim** — update
both when refreshing.

**Per-query math vs real-world spend.** The matrix above is what an
isolated benchmark would measure. Real agent loops with disciplined
Anthropic prompt caching see 50-80% discount on top (cache hits skip
downstream entirely). The realistic-scale anchor in
`docs/eval/SEARCH_MODE_METHODOLOGY.md` walks the natural pairings at
single-power-user volume (~860 turns/mo): tokenmax+Opus ~\$700/mo,
balanced+Sonnet ~\$430/mo, conservative+Haiku ~\$170/mo. Setups WITHOUT
cache-aware prompt layout (frequent prefix churn) see the per-query
matrix dominate — mode + model choice matters more there.

**Resolution chain** (matches the v0.31.12 model-tier pattern at
`src/core/model-config.ts:resolveModel`):

    per-call SearchOpts → per-key config (search.cache.enabled, …) →
      MODE_BUNDLES[search.mode] → MODE_BUNDLES.balanced (fallback)

Mode resolution lives in **bare `hybridSearch`** (NOT just the cached wrapper)
per `[CDX-5+6]` in `~/.claude/plans/lets-take-a-look-validated-parrot.md` — so
`gbrain eval replay` and `gbrain eval longmemeval` test the same mode-affected
behavior as the production `query` op.

**Cache-key contamination hotfix `[CDX-4]`:** migration v56 added a
`knobs_hash` column to `query_cache`. The lookup filter is now
`WHERE source_id = $ AND knobs_hash = $ AND embedding similarity < $` so a
tokenmax write (expansion=on, limit=50) can't be served to a conservative
read.

**v0.36.3.0 knobs_hash v=2 → v=3.** The hash now folds the active
embedding column name + provider into the cache key, so a query routed
through `embedding_voyage` (1024d Voyage) can't be served a cache row
written against `embedding` (1536d OpenAI). Existing v=2 rows become
unreachable on first re-query (one-time miss spike on upgrade);
`mode.ts:KNOBS_HASH_VERSION` is the single source of truth.

**Three CLI surfaces:**

    gbrain search modes              # what is running, with per-knob attribution
    gbrain search modes --reset      # clear search.* overrides (mode bundle wins)
    gbrain search stats [--days N]   # cache hit rate, intent mix, budget drops
    gbrain search tune [--apply]     # data-driven recommendations

The install picker fires inside `gbrain init` AFTER `engine.initSchema()`
(non-TTY auto-selects). The upgrade banner fires once via `runPostUpgrade`
in `src/commands/upgrade.ts`, gated by `search.mode_upgrade_notice_shown`.

## Eval discipline (v0.32.3)

Every metric printed by any `gbrain eval *` or `gbrain search stats` command
resolves through `src/core/eval/metric-glossary.ts` so industry terms
(`P@k`, `nDCG@k`, `MRR`, `Jaccard@k`) carry a plain-English line in human
output and a `_meta.metric_glossary` block in JSON output (one block per
response per `[CDX-25]`, NOT sibling `_gloss` fields).

The full methodology — datasets, sample selection, pre-registered
expectations, threats to validity, paired-bootstrap + Bonferroni p-value
discipline `[CDX-14]` — lives in `docs/eval/SEARCH_MODE_METHODOLOGY.md`.
Auto-regenerated `docs/eval/METRIC_GLOSSARY.md` is CI-guarded against
drift (`scripts/check-eval-glossary-fresh.sh`).

Per-run records land at `<repo>/.gbrain-evals/eval-results.jsonl` per
`[CDX-23]`. The user's personal `~/.gbrain` brain is NEVER touched —
audit trail lives in the source repo's git history.

## Skills

Read the skill files in `skills/` before doing brain operations. GBrain ships 29 skills
organized by `skills/RESOLVER.md` (`AGENTS.md` is also accepted as of v0.19):

**Original 8 (conformance-migrated):** ingest (thin router), query, maintain, enrich,
briefing, migrate, setup, publish.

**Brain skills (ported from an upstream agent fork):** signal-detector, brain-ops, idea-ingest, media-ingest,
meeting-ingestion, citation-fixer, repo-architecture, skill-creator, daily-task-manager.

**Operational + identity:** daily-task-prep, cross-modal-review, cron-scheduler, reports,
testing, soul-audit, webhook-transforms, data-research, minion-orchestrator. As of
v0.20.4, `minion-orchestrator` is the single unified skill for both lanes of background
work (shell jobs via `gbrain jobs submit shell`, LLM subagents via `gbrain agent run`) ...
the prior `gbrain-jobs` skill was merged in, Preconditions are shared, and trigger
routing is narrowed to what the skill actually covers.

**Skillify loop (v0.19):** skillify (the markdown orchestration), skillpack-check
(agent-readable health report).

**Routing-table compression (v0.32.3.0):** `skills/functional-area-resolver/` —
two-layer dispatch pattern for shrinking large AGENTS.md / RESOLVER.md files
(>=12KB) without losing routing accuracy. Replaces one row per skill with one
entry per functional area, where each area declares its sub-skills in a
`(dispatcher for: ...)` clause. The static-prompt analog of hierarchical agent
routing (AnyTool [arXiv:2402.04253](https://arxiv.org/abs/2402.04253), RAG-MCP
[arXiv:2505.03275](https://arxiv.org/html/2505.03275v1), Anthropic Agent Skills
progressive disclosure). Empirically validated across Opus 4.7 / Sonnet 4.6 /
Haiku 4.5: +13 to +17pp over the verbose baseline at 48% the size (25KB → 13KB
on a real fork). The `(dispatcher for: ...)` clause is the load-bearing signal
— strip it and lenient accuracy collapses to 41.7% on Sonnet (the
`resolver-of-resolvers` ablation case). A/B eval surface lives at
`evals/functional-area-resolver/` (outside `skills/` deliberately so the
skillpack bundler doesn't ship eval infrastructure to downstream installs):
gateway-routed TypeScript harness, 20 training + 5 held-out fixtures, strict +
lenient scoring, three committed cross-model receipts in `baseline-runs/`.
Receipt header binds (model, prompt_template_hash, fixtures_hash, harness_sha,
ts) so future contributors can verify reproduction. Companion `rescore.mjs`
re-scores existing JSONL with lenient tolerance for zero API cost. Reproduce
with `cd evals/functional-area-resolver && node harness.mjs --model
{opus|sonnet|haiku}` (~$0.30–1.70 per model). Nine v0.33.x follow-up TODOs
filed for held-out corpus growth, cross-vendor verification, hierarchical
area-of-areas, embedding-based pre-router, and the run-1 vs run-2
prompt-design ablation methodology.

**Operational health (v0.19.1):** smoke-test (8 post-restart health checks with auto-fix
for Bun, CLI, DB, worker, Zod CJS, gateway, API key, brain repo; user-extensible via
`~/.gbrain/smoke-tests.d/*.sh`).

**Conventions:** `skills/conventions/` has cross-cutting rules (quality, brain-first,
model-routing, test-before-bulk, cross-modal). `skills/_brain-filing-rules.md` and
`skills/_output-rules.md` are shared references.

## Bulk-action progress reporting

All bulk commands (doctor, embed, import, export, sync, extract, migrate,
repair-jsonb, orphans, check-backlinks, lint, integrity auto, eval, files
sync, and apply-migrations) stream progress through the shared reporter
at `src/core/progress.ts`. Agents get heartbeats within 1 second of every
iteration regardless of how slow the underlying work is.

Rules:
- Progress always writes to **stderr**. Stdout stays clean for data output
  (`--json` payloads, final summaries, JSON action events from `extract`).
- Non-TTY default: plain one-line-per-event human text. JSON requires the
  explicit `--progress-json` flag.
- Global flags (`--quiet`, `--progress-json`, `--progress-interval=<ms>`)
  are parsed by `src/core/cli-options.ts` BEFORE command dispatch.
- Phase names are machine-stable `snake_case.dot.path` (e.g.
  `doctor.db_checks`, `sync.imports`). Documented in
  `docs/progress-events.md`; additive changes only.
- `scripts/check-progress-to-stdout.sh` is a CI guard that fails the build
  if any new code writes `\r` progress to stdout. Wired into `bun run test`.
- Minion handlers pass `job.updateProgress` as the `onProgress` callback
  to core functions (DB-backed primary progress channel); stderr from
  `jobs work` stays coarse for daemon liveness only.

When wiring a new bulk command: `import { createProgress } from '../core/progress.ts'`
and `import { getCliOptions, cliOptsToProgressOptions } from '../core/cli-options.ts'`.
Create a reporter with `createProgress(cliOptsToProgressOptions(getCliOptions()))`,
`start(phase, total?)` before the loop, `tick()` inside it, `finish()` after.
For single long-running queries, use `startHeartbeat(reporter, note)` with a
try/finally to guarantee cleanup. Never call `process.stdout.write('\r...')`
in bulk paths, the CI guard will fail the build.

## Capturing test output (NEVER pipe through `tail` / `head`)

**Iron rule:** when running `bun test`, `bun run test:e2e`, `bun run typecheck`,
or any other test/check command, redirect to a file FIRST, then `tail` the file
separately:

```bash
# RIGHT — full output preserved, real exit code visible
bun test > /tmp/ship_units.txt 2>&1
echo "EXIT=$?"
tail -50 /tmp/ship_units.txt
grep -E '(fail\)|✗|error:' /tmp/ship_units.txt | head -30
```

```bash
# WRONG — exit code is `tail`'s (always 0), failures truncated, ship gates fail open
bun test 2>&1 | tail -10
```

The pipe form silently breaks /ship Step T1 (test failure ownership triage) and
the test verification gate (Step 16) because:
- `$?` after a pipe is the LAST command's exit code (`tail` → 0), not bun's
- bun prints failure details before the summary line, so `tail -N` drops them
- Step T1 needs the full failure list to classify in-branch vs pre-existing

This bit us during v0.26.2 ship: `bun test 2>&1 | tail -10` reported "3911 pass / 23 fail"
but no failure details survived, forcing a 23-minute re-run to triage.

Apply the same pattern to any long-running command whose exit code matters:
`bun run typecheck`, `bun run ci:local`, migration runs, eval suites, etc.
For background tasks (`run_in_background: true`), the harness captures the exit
file separately — use it via the bg task's `<id>.exit` file, not the streamed
output.

## Build

`bun build --compile --outfile bin/gbrain src/cli.ts`

## Version locations (single source of truth: `VERSION` file)

Every release advances the version in **five files at once**. Keep these in
sync. `/ship` enforces this via Step 12's idempotency check (VERSION vs
package.json drift), but the canonical list lives here so future runs and
the auto-update agent know where to look.

**Version format is mandatory: `MAJOR.MINOR.PATCH.MICRO` (four numeric
segments, dot-separated, no leading `v`).** Every new release MUST use the
4-segment form. The `.MICRO` slot is the dot-suffix follow-up channel: when
a release ships its commit subject ahead of its VERSION bump (e.g. PR #795
landing as `v0.31.4` without bumping the file), the corrective ship lands
as `0.31.4.1` rather than churning the patch number to `0.31.5`. Suffixes
like `-fixwave` are still allowed as needed (`0.31.1.1-fixwave`), but the
four numeric segments are required first. Historical 3-segment versions
(`0.31.3`, `0.22.1`) remain valid in `git log` and migration filenames
(`skills/migrations/v0.21.0.md`); do NOT rewrite them. Going forward only.

**Required (every release must update all five):**

| File | What lives there | Format |
|---|---|---|
| `VERSION` | The single source of truth. Read first by `/ship`, the binary, and CI version-gate. | Bare 4-segment string `MAJOR.MINOR.PATCH.MICRO` (e.g. `0.31.4.1`), no leading `v`. |
| `package.json` | Bun/npm package version. `gbrain --version` reads it via the compiled binary's bundled package metadata. CI version-gate cross-checks this against `VERSION` and fails if they drift. | `"version": "0.31.4.1"` |
| `CHANGELOG.md` | Top entry header `## [0.31.4.1] - YYYY-MM-DD` plus the "To take advantage of v0.31.4.1" block. | Standard Keep-a-Changelog header. |
| `TODOS.md` | Any TODO entries that mention "follow-up from vX.Y.Z.W" use the version of the release that filed them. Update only when filing NEW follow-up TODOs. | Inline `vX.Y.Z.W` references in TODO bodies. |
| `CLAUDE.md` | The Key Files section's per-file annotations carry `vX.Y.Z.W (#NNN)` tags noting which release introduced a behavior. Update whenever a wave's annotations get folded in. | Inline `vX.Y.Z.W (#NNN, contributed by @user)` references. |

**Auto-derived (no manual edit; refreshed by their own commands):**

- `bun.lock` — root-package version is auto-pinned from `package.json`. After
  bumping `package.json`, run `bun install` to refresh the lockfile.
- `llms-full.txt` / `llms.txt` — auto-generated documentation bundles. **Any
  CLAUDE.md edit MUST be followed by `bun run build:llms` in the same commit
  (or a follow-up commit before push).** The committed bundles are checked
  against fresh generator output by `test/build-llms.test.ts`, which runs in
  CI shard 1. If you edited CLAUDE.md and didn't regenerate, CI will fail.
  This has bitten the wave 3 times — every CLAUDE.md edit gets a `bun run
  build:llms` chaser, no exceptions. (The `verify` gate doesn't run this
  test; only the full unit suite does. So `bun run typecheck` clean is NOT
  enough to know you can push after a CLAUDE.md edit.)

**Historical (DO NOT bump on release):**

- `skills/migrations/v0.21.0.md` — migration files use the version they
  shipped FROM as their filename. v0.21.0's migration always says v0.21.0.
- `src/commands/migrations/v0_21_0.ts` — same: migration code references
  the schema version it migrates to.
- `test/migrations-v0_21_0.test.ts`, `test/migration-orchestrator-v0_21_0.test.ts`,
  `test/migrate.test.ts` — migration tests reference historical migration
  versions; these are correct as-is and should not move.
- `src/core/db.ts`, `src/core/migrate.ts`, `src/core/import-file.ts`,
  `src/commands/reindex-code.ts` — code comments cite the release that
  introduced a feature. Once written, these are historical record.
- `README.md` — references the latest published feature names by version
  (e.g. "v0.21.0 Code Cathedral"); update only when the README's marketing
  copy is intentionally being refreshed, NOT on every micro/patch bump.

**The /ship workflow's version idempotency check:** Step 12 reads
`VERSION` and `package.json`, classifies as FRESH / ALREADY_BUMPED /
DRIFT_STALE_PKG / DRIFT_UNEXPECTED, and refuses to proceed on
DRIFT_UNEXPECTED. This is why the two must move together.

**The CI version-gate** rejects pushes where `VERSION` and
`package.json` disagree, OR where `VERSION` is not strictly greater
than master's VERSION. If a queue collision claims your version on
master before yours lands, /ship's queue-aware allocator (Step 12)
will detect drift and re-bump on the next run.

### Mandatory version-consistency audit (run after EVERY merge or commit that touches VERSION, package.json, or CHANGELOG)

**The trio MUST agree.** Every merge from master will hit conflicts on
VERSION + package.json + CHANGELOG.md because master ships its own
version bumps. Auto-merge sometimes resolves these silently in unexpected
ways. After any merge, branch update, or version-related edit, run this
audit. It's three lines and never lies:

```bash
echo "VERSION:     $(cat VERSION)"
echo "package.json: $(node -e 'process.stdout.write(require("./package.json").version)')"
grep -E "^## \[" CHANGELOG.md | head -1
```

All three MUST show the same `MAJOR.MINOR.PATCH.MICRO`. If any one
disagrees, you have not finished the merge. Fix it before pushing or
shipping. There is no situation in which "I'll fix it next push" is OK,
because:

- A green local test run with mismatched VERSION/package.json still
  fails the CI version-gate.
- A green CHANGELOG entry under the wrong version header silently lies
  to release-notes consumers.
- /ship's Step 12 idempotency check classifies a mismatch as
  `DRIFT_UNEXPECTED` and HALTS — but only if you remember to run /ship
  before pushing. Manual `git push` skips the check.

### Merge-conflict recovery procedure (memorize this)

When `git merge origin/master` reports conflicts on VERSION,
package.json, or CHANGELOG.md, resolve in this exact order:

1. **VERSION** — overwrite with the wave's version (`echo -n "X.Y.Z.W"
   > VERSION`). Highest semver wins; do NOT take master's lower version.
2. **package.json** — strip the conflict markers, keep the wave's
   version line. Sed pattern:
   `sed -i.bak '/^<<<<<<< HEAD$/d; /^=======$/,/^>>>>>>> /d' package.json && rm package.json.bak`
   (assumes ours is above the `=======`).
3. **CHANGELOG.md** — strip ALL three conflict markers; both your entry
   and master's entry stay. Sed pattern:
   `sed -i.bak '/^<<<<<<< HEAD$/d; /^=======$/d; /^>>>>>>> origin\/master$/d' CHANGELOG.md && rm CHANGELOG.md.bak`
   Then verify your entry is the topmost `## [X.Y.Z.W]` and master's
   newer-than-yours entries (if any) sit below.
4. **Run the 3-line audit above.** If it doesn't show your version on
   all three lines, you missed a marker.
5. **Run `bun install`** to refresh `bun.lock` against the resolved
   `package.json`. Stage and commit if it changed.
6. **Run `bun run typecheck`** before committing the merge.
7. Only THEN run `git commit` for the merge.

If the audit shows drift after step 4, do NOT proceed to step 5. Re-run
steps 1-3 against the actual file content; you missed a marker or
resolved one in the wrong direction.

**Anti-pattern to avoid:** Resolving via `git checkout --ours package.json`
and `git checkout --theirs scripts/test-shard.sh` mixed in the same
commit. The selective directional resolution is fine, but on
VERSION/package.json/CHANGELOG specifically, ALWAYS use the explicit
`echo > VERSION` + sed-strip-markers pattern above. The directional
checkout flags have bitten us when the conflict shape was unexpected
(e.g. master stripped a section we expected to keep).

### Pre-push gate (manual; tighten when you remember to)

Before any `git push` of a merge commit, run the audit one more time:

```bash
echo "VERSION:     $(cat VERSION)"
echo "package.json: $(node -e 'process.stdout.write(require("./package.json").version)')"
grep -E "^## \[" CHANGELOG.md | head -1
```

If you've been editing the branch via `/ship` you can rely on Step 12's
idempotency check. If you've been editing manually (merge resolution,
conflict fix, version bump), the audit is the last line of defense
before CI yells at you.

## Conductor branch-name = workspace-name (IRON RULE)

Conductor workspaces expect the git branch name to match the workspace
directory name. When they disagree, Conductor silently fails to render the
PR view + show ship state, leading to "did you actually push?" confusion.

**Check this FIRST on every ship and BEFORE creating any PR:**

```bash
WORKSPACE=$(basename "$PWD")              # e.g. puebla-v4
BRANCH=$(git branch --show-current)        # e.g. garrytan/gstack-requests
case "$BRANCH" in
  */"$WORKSPACE") echo "OK: branch tail matches workspace" ;;
  "$WORKSPACE")   echo "OK: branch == workspace" ;;
  *)              echo "MISMATCH: branch=$BRANCH workspace=$WORKSPACE — RENAME BEFORE SHIPPING" ;;
esac
```

If MISMATCH (branch is `garrytan/foo` but workspace is `puebla-v4`):

```bash
# Rename local, push under new name, delete old remote (and old PR if it
# was already created — github auto-closes it when head ref dies).
git branch -m garrytan/<workspace-name>
git push -u origin garrytan/<workspace-name>
git push origin --delete <old-branch-name>
# If a PR existed against the old branch:
#   gh pr comment <old-pr> --body "Superseded by #<new>: branch renamed to match Conductor workspace."
#   gh pr create --base master --title "..." --body "..."  # recreate from renamed branch
```

Caught the hard way on v0.41.9.0 ship: workspace `puebla-v4` but branch
`garrytan/gstack-requests` produced PR #1439 that Conductor wouldn't
display. Renamed to `garrytan/puebla-v4`; recreated as #1440.

The /ship workflow's Step 1 should be augmented to run the mismatch
check; until that lands upstream, ALWAYS run the check above before
`/ship` invokes its first push or PR-create step.

## Pre-ship requirements

Before shipping (/ship) or reviewing (/review), always run the full test suite.
Two equivalent paths:

**Path A — local CI gate (recommended, v0.23.1+):**
- `bun run ci:local` runs the entire stack inside Docker: gitleaks (host), unit
  tests with `DATABASE_URL` unset, and all 29 E2E files sequentially against a
  fresh pgvector container. Stronger than PR CI's 2-file Tier 1 set; closer to
  what nightly Tier 1 catches. Spins up + tears down postgres automatically via
  `docker-compose.ci.yml`. Override the host port with
  `GBRAIN_CI_PG_PORT=5435 bun run ci:local` if 5434 collides.
- `bun run ci:local:diff` runs only the E2E files matched by the diff selector
  (`scripts/select-e2e.ts`), falling back to all 29 on unmapped src/ paths or
  schema/skills/package.json changes. Fast iteration during a focused branch.

**Path B — manual lifecycle (still supported):**
- `bun test` — unit tests (no database required)
- Follow the "E2E test DB lifecycle" steps above to spin up the test DB,
  run `bun run test:e2e`, then tear it down.

Both must pass. Do not ship with failing E2E tests. Do not skip E2E tests.

**Always run typecheck before pushing.** `bun test` (the bun runner)
skips TypeScript type checking — it only enforces runtime behavior.
Three ways to actually gate on types:

1. `bun run test` (npm script in `package.json`) — includes `bun run typecheck`
   plus the four shell pre-checks (`check-jsonb-pattern.sh`,
   `check-progress-to-stdout.sh`, `check-trailing-newline.sh`,
   `check-wasm-embedded.sh`) before the runner. Use this mid-branch.
2. `bun run typecheck` — `tsc --noEmit` standalone. Fast (~5s on this repo).
3. `bun run ci:local` — the full local CI gate from Path A.

The trap is: writing a new test, running `bun test test/foo.test.ts`,
seeing it pass, pushing — and CI's separate typecheck stage rejects an
invalid type literal that the runner accepted. Caught one of these
shipping the v0.23.2 round-trip E2E (`type: 'reflection'` is not a
member of `PageType`). Run `bun run typecheck` once before push, even
when only test files changed.

## Post-ship requirements (MANDATORY)

After EVERY /ship, you MUST run /document-release. This is NOT optional. Do NOT
skip it. Do NOT say "docs look fine" without running it. The skill reads every .md
file in the project, cross-references the diff, and updates anything that drifted.

If /ship's Step 8.5 triggers document-release automatically, that counts. But if
it gets skipped for ANY reason (timeout, error, oversight), you MUST run it manually
before considering the ship complete.

Files that MUST be checked on every ship:
- README.md — does it reflect new features, commands, or setup steps?
- CLAUDE.md — does it reflect new files, test files, or architecture changes?
- CHANGELOG.md — does it cover every commit?
- TODOS.md — are completed items marked done?
- docs/ — do any guides need updating?

A ship without updated docs is an incomplete ship. Period.

## CHANGELOG + VERSION are branch-scoped

**VERSION and CHANGELOG describe what THIS branch adds vs master, not how we got
here.** Every feature branch that ships gets its own version bump and CHANGELOG
entry. The entry is product release notes for users; it is not a log of internal
decisions, review rounds, or codex findings.

**Write the CHANGELOG entry at /ship time, not during development.** Mid-branch
iterations, review rounds (CEO/Eng/Codex/DX), and implementation detours belong
in the plan file at `~/.claude/plans/`, not in the CHANGELOG. One unified entry
per branch, covering what the branch added vs the base branch.

**Never edit a CHANGELOG entry that already landed on master.** If master has
v0.18.2 and your branch adds features, bump to the next version (v0.19.0, not
editing master's v0.18.2). When merging master into your branch, master may
bring new CHANGELOG entries above yours — push your entry above master's
latest and verify:

- Does CHANGELOG have your branch's own entry separate from master's entries?
- Is VERSION higher than master's VERSION?
- Is your entry the topmost `## [X.Y.Z]` entry?
- `grep "^## \[" CHANGELOG.md` shows a contiguous version sequence?

If any answer is no, fix it before continuing.

**CHANGELOG is for users, not contributors.** Write like product release notes:

- Lead with what the user can now **do** that they couldn't before. Sell the capability.
- Plain language, not implementation details. "You can now..." not "Refactored the..."
- **Never mention internal artifacts**: plan file IDs, decision tags (D-CX-#, F-ENG-#),
  review rounds, codex findings, subcontractor credits. These are invisible to users.
- Put contributor-facing changes in a separate `### For contributors` section at the bottom.
- Every entry should make someone think "oh nice, I want to try that."

**What to omit:**
- "Codex caught X that the CEO review missed" — private process detail.
- "D-CX-3 split errors/warnings" — tag is meaningless to users; name the feature instead.
- "Fix-wave PR #N supersedes #M" — supersede chains belong in PR bodies, not release notes.
- "215 new cases, 3 decisions applied, 7 reviews cleared" — these are planning-mode metrics.

**What to keep:**
- The user-facing change: what commands exist now, what flag was added, what behavior fixed.
- Numbers that mean something to the user: TTHW, commands that timed out before, detection counts.
- Upgrade instructions: `gbrain upgrade` + any manual step if needed.
- Credit to external contributors when a community PR was incorporated.

## CHANGELOG voice + release-summary format

**IRON RULE: the CHANGELOG describes what the user gets, not how the work
happened.** Nobody reading release notes cares that codex caught a bug, that
the plan went through CEO + eng review, that the migration was originally
numbered v68 and renumbered to v79 during master merge, or that two
review rounds caught architectural mistakes. The reader cares what
`gbrain brainstorm` does and how to use it. If a fact only exists because
of the development process, it does NOT belong in the CHANGELOG.

**Specifically forbidden in CHANGELOG entries:**

- Any mention of review processes (CEO review, eng review, codex review,
  plan-eng-review, outside voice, adversarial review, autoplan, /review).
- "What we caught and fixed before merging" sections. Bugs found pre-merge
  are not changes — they're things that didn't ship.
- Plan file references, plan IDs, plan decision tags (D1, D14, D-CDX-3).
- Migration version drama ("originally v68", "renumbered to v77", "claimed
  by parallel waves") — just say "Migration v79 adds X." If the user
  cares about migration ordering, they read the diff.
- Round counts, finding counts, decision counts ("25 findings across 2
  rounds", "8 architectural decisions", "5/6 expansions accepted").
- Names of internal collaborators ("codex caught", "the reviewer flagged",
  "Claude noticed").
- "Plan + reviews" summary bullets. The plan lives in `~/.claude/plans/`;
  if a future reader wants the backstory they can grep there.
- Any wording that frames a shipped feature as a *recovery* from a planning
  mistake ("the first plan was wrong", "we corrected the approach", "the
  shipped version supersedes the original design").

**Smell test:** read the entry as a stranger who has never touched gbrain.
If any sentence makes them think "why are you telling me this?", cut it.
Every sentence in the release-summary AND in the itemized changes must
answer one of three questions: *What can I now do? How do I use it? What
should I watch for after I upgrade?*

Every version entry in `CHANGELOG.md` MUST start with a release-summary section in
the GStack/Garry voice — one viewport's worth of prose + tables that lands like a
verdict, not marketing. The itemized changelog (subsections, bullets, files) goes
BELOW that summary, separated by a `### Itemized changes` header.

The release-summary section gets read by humans, by the auto-update agent, and by
anyone deciding whether to upgrade. The itemized list is for agents that need to
know exactly what changed.

### Release-summary template

**Iron rule: lead ELI10, get precise after.** The first ~150 words of every entry
must be readable by someone who does NOT know gbrain's internals. No file paths,
no function names, no internal constants, no acronyms (no "RRF", no "knobsHash",
no "MODE_BUNDLES", no "CDX-4"), no jargon that requires reading the codebase to
parse. Lead with the user-visible behavior change, in everyday English, like
you're explaining it to a smart engineer who has never opened the repo.

THEN, once the reader knows what shipped and why they'd care, drill into the
precise details: real file paths, real function names, real config keys, real
numbers. The precision part is required (the entry is also the technical record
of what changed), but it lives AFTER the plain-English lead, never before it.

The shape:

1. **One-line bold headline.** What changed for the user, in human English. No
   jargon. No internal terms. Example good: "Your search stops boosting weak
   pages just because they have a lot of links pointing at them." Example bad:
   "PostFusionOpts gains floorRatio; KNOBS_HASH_VERSION bumped 2→3."
2. **Plain-English opener** (~3-5 sentences). Describe the problem this fixes in
   everyday terms. Pretend the reader has a brain full of meeting notes and
   people pages and wants to know if this release helps them. Concrete example
   beats abstract description.
3. **A "How to turn it on" or "How to use it" section** with paste-ready
   commands. Real flags, real config keys. This is where precision starts.
4. **A "What you'd see in a concrete example" or "The X numbers that matter"
   section** with a table. Use everyday-language column headers ("Page",
   "Match quality", "Has many backlinks?") even when the underlying mechanism
   is technical. The table teaches what the feature does without requiring the
   reader to understand how.
5. **A "What's safe to know about" or "Things to watch" section** for caveats,
   side effects, cache invalidation, mid-deploy notes. Still in plain language.
6. **A "What we caught and fixed before merging" section** if the work went
   through review (CEO/eng/codex/outside-voice). Translate review findings into
   plain English. "We caught a stale-cache bug" beats "knobsHash() did not
   include floorRatio in the v=2 hash input."
7. **`### Itemized changes`** (precision lives here). File paths, function
   names, types, constants, line numbers. This section is for engineers who
   need to know exactly what moved.

Voice rules (apply throughout):
- No em dashes (use commas, periods, "...").
- No AI vocabulary (delve, robust, comprehensive, nuanced, fundamental, etc.) or
  banned phrases ("here's the kicker", "the bottom line", etc.).
- Real numbers, real file names, real commands AFTER the ELI10 lead. Not "fast"
  but "~30s on 30K pages." In the ELI10 lead, "fast enough that you won't
  notice" or "~30 seconds even on a big brain."
- Short paragraphs, mix one-sentence punches with 2-3 sentence runs.
- Connect to user outcomes: "the agent does ~3x less reading" beats "improved
  precision."
- Be direct about quality. "Well-designed" or "this is a mess." No dancing.

**The smell test:** if someone who has never opened gbrain reads the first 150
words and walks away knowing what shipped and whether they care, the entry
passes. If they need to grep the codebase to follow along, rewrite the lead.

**Canonical examples in this CHANGELOG:** v0.35.6.0 (floor-ratio gate, written
ELI10-lead-first), v0.34.4.0 (embed stale fix wave). Use those shapes when in
doubt. Avoid the shape of entries that lead with internal constants or release
mechanics; those exist in older history but should not be the model for new
work.

Source material to pull from:
- CHANGELOG.md previous entry for prior context
- Latest `gbrain-evals/docs/benchmarks/[latest].md` for headline numbers (sibling repo)
- Recent commits (`git log <prev-version>..HEAD --oneline`) for what shipped
- Don't make up numbers. If a metric isn't in a benchmark or production data, don't
  include it. Say "no measurement yet" if asked.

Target length: ~250-350 words for the summary. Should render as one viewport.

### "To take advantage of v[version]" block (required, v0.13+)

After the release-summary and BEFORE `### Itemized changes`, every `## [X.Y.Z]`
entry MUST include a human-readable self-repair block under the heading
`## To take advantage of v[version]`.

Why: `gbrain upgrade` runs `gbrain post-upgrade` which runs `gbrain apply-migrations`.
This chain has a known weak link — `upgrade.ts` catches post-upgrade failures as
best-effort (so the binary still works). When that chain silently fails, users end
up with half-upgraded brains. The self-repair block gives them a paste-ready
recovery path; the v0.13+ `~/.gbrain/upgrade-errors.jsonl` trail + `gbrain doctor`
integration close the loop.

Template (adapt the verify commands per release):

```markdown
## To take advantage of v[version]

`gbrain upgrade` should do this automatically. If it didn't, or if `gbrain doctor`
warns about a partial migration:

1. **Run the orchestrator manually:**
   ```bash
   gbrain apply-migrations --yes
   ```
2. **Your agent reads `skills/migrations/v[version].md` the next time you interact with it.**
   [One sentence on whether headless agents need manual action, or whether the
   orchestrator already handled the mechanical side.]
3. **Verify the outcome:**
   ```bash
   [release-specific verify commands, e.g. `gbrain graph ... --depth 2`]
   gbrain stats
   ```
4. **If any step fails or the numbers look wrong,** please file an issue:
   https://github.com/garrytan/gbrain/issues with:
   - output of `gbrain doctor`
   - contents of `~/.gbrain/upgrade-errors.jsonl` if it exists
   - which step broke

   This feedback loop is how the gbrain maintainers find fragile upgrade paths. Thank you.
```

**Skip this block** for patches that are pure bug fixes with zero user-facing action
(rare). If the release has a schema migration, data backfill, or new feature the
user needs to verify, the block is required.

The v0.13.0 entry in CHANGELOG.md is the canonical example.

### Itemized changes (the existing rules)

Below the release summary, write `### Itemized changes` and continue with the
detailed subsections (Knowledge Graph Layer, Schema migrations, Security hardening,
Tests, etc.). Same rules as before:

- Lead with what the user can now DO that they couldn't before
- Frame as benefits and capabilities, not files changed or code written
- Make the user think "hell yeah, I want that"
- Bad: "Added GBRAIN_VERIFY.md installation verification runbook"
- Good: "Your agent now verifies the entire GBrain installation end-to-end, catching
  silent sync failures and stale embeddings before they bite you"
- Bad: "Setup skill Phase H and Phase I added"
- Good: "New installs automatically set up live sync so your brain never falls behind"
- **Always credit community contributions.** When a CHANGELOG entry includes work from
  a community PR, name the contributor with `Contributed by @username`. Contributors
  did real work. Thank them publicly every time, no exceptions.

### Reference: v0.12.0 entry as canonical example

The v0.12.0 entry in CHANGELOG.md is the canonical example of the format. Match its
structure for every future version: bold headline, lead paragraph, "numbers that
matter" with BrainBench-style before/after table, "what this means" closer, then
`### Itemized changes` with the detailed sections below.

## Version migrations

Create a migration file at `skills/migrations/v[version].md` when a release
includes changes that existing users need to act on. The auto-update agent
reads these files post-upgrade (Section 17, Step 4) and executes them.

**You need a migration file when:**
- New setup step that existing installs don't have (e.g., v0.5.0 added live sync,
  existing users need to set it up, not just new installs)
- New SKILLPACK section with a MUST ADD setup requirement
- Schema changes that require `gbrain init` or manual SQL
- Changed defaults that affect existing behavior
- Deprecated commands or flags that need replacement
- New verification steps that should run on existing installs
- New cron jobs or background processes that should be registered

**You do NOT need a migration file when:**
- Bug fixes with no behavior changes
- Documentation-only improvements (the agent re-reads docs automatically)
- New optional features that don't affect existing setups
- Performance improvements that are transparent

**The key test:** if an existing user upgrades and does nothing else, will their
brain work worse than before? If yes, migration file. If no, skip it.

Write migration files as agent instructions, not technical notes. Tell the agent
what to do, step by step, with exact commands. See `skills/migrations/v0.5.0.md`
for the pattern.

## Migration is canonical, not advisory

GBrain's job is to deliver a canonical, working setup to every user on upgrade.
Anything that looks like a "host-repo change" — AGENTS.md, cron manifests,
launchctl units, config files outside `~/.gbrain/` — is a GBrain migration
step, not a nudge we leave for the host-repo maintainer. Migrations edit host
files (with backups) to make the canonical setup real. Exceptions: changes
that require human judgment (content edits, renames that break semantics,
host-specific handler registration where shell-exec would be an RCE surface).
Everything mechanical ships in the migration.

**Test:** if shipping a feature requires a sentence that starts with "in
your AGENTS.md, add…" or "in your cron/jobs.json, rewrite…", the migration
orchestrator should be doing that edit, not the user.

**The exception is host-specific code.** For custom Minion handlers
(host-specific integrations like inbox sweeps or third-party API scanners), shipping them as a
data file the worker would exec is an RCE surface. Those get registered in
the host's own repo via the plugin contract (`docs/guides/plugin-handlers.md`);
the migration orchestrator emits a structured TODO to
`~/.gbrain/migrations/pending-host-work.jsonl` + the host agent walks the
TODOs using `skills/migrations/v0.11.0.md` — stays host-agnostic, still
canonical.

## Privacy rule: scrub real names from public docs

**Never reference real people, companies, funds, or private agent names in any
public-facing artifact.** Public artifacts include: `CHANGELOG.md`, `README.md`,
`docs/`, `skills/`, PR titles + bodies, commit messages, and comments in checked-in
code. Query examples, benchmark stories, and migration guides MUST use generic
placeholders.

Why: gbrain runs a personal knowledge brain containing notes on real people and
real companies (YC founders, portfolio companies, funds, investors, meeting
attendees). When a doc copies a query like `gbrain graph diana-hu --depth 2` or
names a specific agent fork like `Wintermute`, that real name gets indexed by
search engines, surfaced in cross-references, and distributed with every release.

**Name mapping** to use in examples:
- Agent forks → `your agent fork`, `a downstream agent`, or `agent-fork`
- Example person → `alice-example`, `charlie-example`, or `a-founder`
- Example company → `acme-example`, `widget-co`, or `a-company`
- Example fund → `fund-a`, `fund-b`, `fund-c`
- Example deal → `acme-seed`, `widget-series-a`
- Example meeting → `meetings/2026-04-03` (generic date is fine)
- Example user → `you` or `the user`, never a proper name

**Specific rule: never say `Wintermute` in any CHANGELOG, README, doc, PR, or
commit message.** When the temptation is to illustrate with the real fork name:
- Reader-facing copy → `your OpenClaw` (covers Wintermute, Hermes, AlphaClaw,
  and any other downstream OpenClaw deployment in one term the reader already
  recognizes).
- First-person / origin-story copy → `Garry's OpenClaw` (honest that this is
  the production deployment driving the feature, without exposing the private
  agent's name).

`Wintermute` may appear in private artifacts (scratch plans under
`~/.gstack/projects/…`, memory files, conversation transcripts, CEO-review
plans) — those aren't distributed. Anything checked into this repo or shipped
in a release must use the OpenClaw phrasing above. Sweeping a stale reference
is a small clean-up PR, not a debate.

**When in doubt, ask yourself:** "Would this query reveal private information
about the user's contacts, investments, or portfolio if it were read by a
stranger?" If yes, replace with generic placeholders.

**Illustrative API examples with household-brand companies** (Stripe, Brex, OpenAI,
GitHub, etc.) are fine — they're public entities, not contacts in anyone's brain.
Do not confuse illustrative API examples with queries that reveal real
relationships.

## Responsible-disclosure rule: don't broadcast attack surface in release notes

**When a release fixes a security gap or a user-impacting bug, describe the fix
functionally. Do not enumerate the attack surface, quantify the exposure window,
or highlight the most sensitive records by name in public-facing artifacts.**

Public-facing artifacts include: `CHANGELOG.md`, `README.md`, `docs/`, PR titles
and bodies, commit messages, GitHub issue titles and comments, release pages,
tweets, blog posts.

**Don't write:**
- "10 tables were publicly readable by the anon key for months, including X, Y, Z"
- "X and Y are the most sensitive ones"
- "N tables exposed. Fix: enable RLS on these specific tables: ..."

**Do write:**
- "Security hardening pass. Fresh installs secure by default. Existing brains
  brought to the same bar automatically on upgrade."
- "If `gbrain doctor` still flags anything after upgrade, the message names each
  table and gives the exact fix."

Why: anyone reading the release page before they've upgraded now has a directed
probe list for unpatched installs. The source code ships the specifics anyway
(`src/schema.sql`, `src/core/migrate.ts`, test fixtures) — reverse engineers can
get them. But the release page is a broadcast channel. Don't hand attackers a
curated list with a banner.

**The test:** if a reader with no prior context could read the release note and
walk away knowing "gbrain at version X has table Y readable by anon key until
they patch," the note is too specific. Rewrite until that's no longer possible.

**What IS fine in public artifacts:**
- The mechanism of the fix ("the check now scans every public table instead of
  a hardcoded allowlist").
- User-facing operator ergonomics (the escape-hatch SQL template, the upgrade
  commands, the breaking-change flag).
- Credit to contributors.
- Generic framing of severity ("security posture tightening pass") without
  quantification.

**What stays in private artifacts (plan files, private memories, internal docs):**
- Specific table names, record counts, exposure duration.
- Which records stand out as highest-risk.
- Detailed before/after tables in the "numbers that matter" format.

If the CEO/Eng review of a plan produces a detailed exposure table, keep it in
the plan file under `~/.claude/plans/` or `~/.gstack/projects/`. Don't copy it
into the CHANGELOG or PR body.

Applies retroactively: if you see a prior CHANGELOG entry naming attack-surface
specifics, scrub it as a small cleanup commit, the same way a stale Wintermute
reference gets swept.

## Schema state tracking

`~/.gbrain/update-state.json` tracks which recommended schema directories the user
adopted, declined, or added custom. The auto-update agent (SKILLPACK Section 17)
reads this during upgrades to suggest new schema additions without re-suggesting
things the user already declined. The setup skill writes the initial state during
Phase C/E. Never modify a user's custom directories or re-suggest declined ones.

## GitHub Actions SHA maintenance

All GitHub Actions in `.github/workflows/` are pinned to commit SHAs. Before shipping
(`/ship`) or reviewing (`/review`), check for stale pins and update them:

```bash
for action in actions/checkout oven-sh/setup-bun actions/upload-artifact actions/download-artifact softprops/action-gh-release gitleaks/gitleaks-action; do
  tag=$(grep -r "$action@" .github/workflows/ | head -1 | grep -o '#.*' | tr -d '# ')
  [ -n "$tag" ] && echo "$action@$tag: $(gh api repos/$action/git/ref/tags/$tag --jq .object.sha 2>/dev/null)"
done
```

If any SHA differs from what's in the workflow files, update the pin and version comment.

## PR descriptions cover the whole branch

Pull request titles and bodies must describe **everything in the PR diff against the
base branch**, not just the most recent commit you made. When you open or update a
PR, walk the full commit range with `git log --oneline <base>..<head>` and write the
body to cover all of it. Group by feature area (schema, code, tests, docs) — not
chronologically by commit.

This matters because reviewers read the PR body to understand what's shipping. If
the body only covers your last commit, they miss everything else and can't review
properly. A 7-commit PR with a body that describes commit 7 is worse than no body
at all — it actively misleads.

When in doubt, run `gh pr view <N> --json commits --jq '[.commits[].messageHeadline]'`
to see what's actually in the PR before writing the body.

## Community PR wave process

Never merge external PRs directly into master. Instead, use the "fix wave" workflow:

1. **Categorize** — group PRs by theme (bug fixes, features, infra, docs)
2. **Deduplicate** — if two PRs fix the same thing, pick the one that changes fewer
   lines. Close the other with a note pointing to the winner.
3. **Collector branch** — create a feature branch (e.g. `garrytan/fix-wave-N`), cherry-pick
   or manually re-implement the best fixes from each PR. Do NOT merge PR branches directly —
   read the diff, understand the fix, and write it yourself if needed.
4. **Test the wave** — verify with `bun test && bun run test:e2e` (full E2E lifecycle).
   Every fix in the wave must have test coverage.
5. **Close with context** — every closed PR gets a comment explaining why and what (if
   anything) supersedes it. Contributors did real work; respect that with clear communication
   and thank them.
6. **Ship as one PR** — single PR to master with all attributions preserved via
   `Co-Authored-By:` trailers. Include a summary of what merged and what closed.

**Community PR guardrails:**
- Always AskUserQuestion before accepting commits that touch voice, tone, or
  promotional material (README intro, CHANGELOG voice, skill templates).
- Never auto-merge PRs that remove YC references or "neutralize" the founder perspective.
- Preserve contributor attribution in commit messages.

## Checking out PRs from garrytan-agents

`garrytan-agents` is the AI-authored PR account and is NOT a collaborator on
this repo. Its PRs live in a fork, so GitHub Actions triggered by
`pull_request` events on those PRs do not receive base-repo secrets. Any CI
job that needs `ANTHROPIC_API_KEY`, `OPENAI_API_KEY`, or similar will fail
with empty-env auth errors, regardless of what's set on the base repo. This
is a GitHub security default, not a config bug.

When the user says "check out <PR link>" and the PR is from `garrytan-agents`
(or any other non-collaborator fork), move the branch into the base repo
before running CI:

1. `gh pr checkout <N>` — pull down the fork's branch. Note the PR number and
   head branch name (`gh pr view <N> --json headRefName --jq .headRefName`).
2. `git push origin HEAD:<branch-name>` — push the same branch to the base
   repo (origin points at `garrytan/gbrain`, not the fork). This is the move
   that gives CI access to secrets.
3. `gh pr close <N> --comment "moving to base-repo branch for secret access"`
   — close the fork PR so the queue stays clean.
4. `gh pr create --base master --head <branch-name>` — open the replacement
   PR from the base-repo branch. **Preserve the original PR's title and body
   verbatim** (`gh pr view <N> --json title,body`); contributor attribution
   moves to a `Co-Authored-By:` trailer if needed.

Why this over alternatives: adding `garrytan-agents` as a collaborator, or
flipping the repo-wide "send secrets to fork PRs" toggle, both broaden
secret distribution to every fork PR from that account or any fork. Moving
the branch keeps secret scope tight to just the one PR being shipped.

## Skill routing

When the user's request matches an available skill, ALWAYS invoke it using the Skill
tool as your FIRST action. Do NOT answer directly, do NOT use other tools first.
The skill has specialized workflows that produce better results than ad-hoc answers.

**NEVER hand-roll ship operations.** Do not manually run git commit + push + gh pr
create when /ship is available. /ship handles VERSION bump, CHANGELOG, document-release,
pre-landing review, test coverage audit, and adversarial review. Manually creating a PR
skips all of these. If the user says "commit and ship", "push and ship", "bisect and
ship", or any combination that ends with shipping — invoke /ship and let it handle
everything including the commits. If the branch name contains a version (e.g.
`v0.5-live-sync`), /ship should use that version for the bump.

Key routing rules:
- Product ideas, "is this worth building", brainstorming → invoke office-hours
- Bugs, errors, "why is this broken", 500 errors → invoke investigate
- Ship, deploy, push, create PR, "commit and ship", "push and ship" → invoke ship
- QA, test the site, find bugs → invoke qa
- Code review, check my diff → invoke review
- Update docs after shipping → invoke document-release
- Weekly retro → invoke retro
- Design system, brand → invoke design-consultation
- Visual audit, design polish → invoke design-review
- Architecture review → invoke plan-eng-review
- Save progress, checkpoint, resume → invoke checkpoint
- Code quality, health check → invoke health

---

## INSTALL_FOR_AGENTS.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/INSTALL_FOR_AGENTS.md

# GBrain Installation Guide for AI Agents

Read this entire file, then follow the steps. Ask the user for API keys when needed.
Target: ~30 minutes to a fully working brain.

## Step 0: If you are not Claude Code

Read `AGENTS.md` at the repo root first. It's the non-Claude-agent operating
protocol (install, read order, trust boundary, common tasks). Claude Code reads
`CLAUDE.md` automatically and can skip ahead.

If you fetched this file by URL without cloning yet, the companion files live at:
- `https://raw.githubusercontent.com/garrytan/gbrain/master/AGENTS.md` — start here
- `https://raw.githubusercontent.com/garrytan/gbrain/master/llms.txt` — full doc map
- `https://raw.githubusercontent.com/garrytan/gbrain/master/llms-full.txt` — same map, inlined

## Step 1: Install GBrain

Default path (Bun is required — gbrain is a Bun + TypeScript runtime):

```bash
curl -fsSL https://bun.sh/install | bash
export PATH="$HOME/.bun/bin:$PATH"
bun install -g github:garrytan/gbrain
```

Verify: `gbrain --version` should print a version number. If `gbrain` is not found,
restart the shell or add the PATH export to the shell profile.

> **If `bun install -g` aborts or `gbrain doctor` reports `schema_version: 0`** (Bun
> occasionally blocks the top-level postinstall hook on global installs, so schema
> migrations don't run automatically), the CLI prints a recovery hint pointing at
> [#218](https://github.com/garrytan/gbrain/issues/218). Run `gbrain apply-migrations --yes`
> to recover. If that doesn't work, fall back to the deterministic install path:
>
> ```bash
> git clone https://github.com/garrytan/gbrain.git ~/gbrain && cd ~/gbrain
> bun install && bun link
> ```

## Step 2: API Keys

Ask the user for these. gbrain defaults to the ZeroEntropy embedding + reranker stack
(as of v0.36.2.0); OpenAI/Voyage are still supported as fallbacks via `gbrain config
set embedding_model <provider:model>`.

```bash
export ZEROENTROPY_API_KEY=ze-...     # default embedding + reranker (v0.36.2.0+)
export OPENAI_API_KEY=sk-...          # fallback for vector search; also used for chat models
export ANTHROPIC_API_KEY=sk-ant-...   # optional, improves search quality via query expansion
```

Save to shell profile or `.env`. Keys are picked up by `gbrain config set` automatically
or can be stored in `~/.gbrain/config.json` (file plane). Without any embedding provider,
keyword search still works. Without Anthropic, search works but skips query expansion.

## Step 3: Create the Brain

```bash
gbrain init                           # PGLite, no server needed
gbrain doctor --json                  # verify all checks pass
```

The user's markdown files (notes, docs, brain repo) are SEPARATE from this tool repo.
Ask the user where their files are, or create a new brain repo:

```bash
mkdir -p ~/brain && cd ~/brain && git init
```

Read `~/gbrain/docs/GBRAIN_RECOMMENDED_SCHEMA.md` and set up the MECE directory
structure (people/, companies/, concepts/, etc.) inside the user's brain repo,
NOT inside ~/gbrain.

## Step 3.5: Confirm search mode with the user (DO NOT SKIP)

`gbrain init` auto-applied a default search mode (`tokenmax` unless your subagent
tier is Haiku-class or no OpenAI key is configured). The init output included the
cost matrix below preceded by `[AGENT]` markers. You must NOT silently accept the
default. Stop and ask the operator.

**Present this matrix verbatim:**

```
Per-query cost @ 10K queries/mo (typical single-user volume):

                  Haiku 4.5     Sonnet 4.6    Opus 4.7
                  ($1/M)        ($3/M)        ($5/M)
  conservative    $40/mo        $120/mo       $200/mo
  balanced        $100/mo       $300/mo       $500/mo
  tokenmax        $200/mo       $600/mo       $1,000/mo

(scales linearly: ×10 for 100K/mo, ÷10 for 1K. 25x corner-to-corner spread.
 Natural diagonal pairings — cheap/cheap → frontier/frontier — span ~4x.)
```

**Ask the operator (paraphrase if needed):**

> Your gbrain just installed with search mode `<auto-applied default>`. This is
> a one-time setup decision that controls retrieval payload size. Which mode
> do you want?
>
>   1) conservative — tight 4K budget, no LLM expansion, 10 chunks max.
>      Best for Haiku subagents, cost-sensitive setups, high-volume loops.
>
>   2) balanced — 12K budget, no expansion, 25 chunks. Sonnet-tier sweet spot.
>
>   3) tokenmax (recommended default — preserves v0.31.x retrieval shape) —
>      no budget, LLM expansion ON, 50 chunks. Best for Opus/frontier models.
>
> Cost depends on BOTH the mode AND the downstream model you run. See the
> matrix above for the 9-cell breakdown.

If the operator picks a non-default mode, run:
```bash
gbrain config set search.mode <mode>
```

If they pick tokenmax AND want to preserve the literal v0.31.x default
(limit=20 instead of tokenmax's 50), also run:
```bash
gbrain config set search.searchLimit 20
```

Verify the choice with `gbrain search modes` before continuing.

**Why this matters:** the cost spread between corners of the matrix is 25x.
An agent that silently accepts the default and starts running queries against
a user who didn't expect tokenmax-class context loads can rack up surprise
spend. Confirm before continuing.

## Step 4: Import and Index

```bash
gbrain import ~/brain/ --no-embed     # import markdown files
gbrain embed --stale                  # generate vector embeddings
gbrain query "key themes across these documents?"
```

## Step 4.5: Wire the Knowledge Graph

If the user already had a brain repo (Step 3 imported existing markdown), backfill
the typed-link graph and structured timeline. This populates the `links` and
`timeline_entries` tables that future writes will maintain automatically.

```bash
gbrain extract links --source db --dry-run | head -20    # preview
gbrain extract links --source db                         # commit
gbrain extract timeline --source db                      # dated events
gbrain stats                                             # verify links > 0
```

For brand-new empty brains, skip this step — auto-link populates the graph as the
agent writes pages going forward. There is nothing to backfill yet.

After this step:
- `gbrain graph-query <slug> --depth 2` works (relationship traversal)
- Search ranks well-connected entities higher (backlink boost)
- Every future `put_page` auto-creates typed links and reconciles stale ones

If a user has a very large brain (>10K pages), `extract --source db` is idempotent
and supports `--since YYYY-MM-DD` for incremental runs.

## Step 5: Load Skills

If you're running an agent platform (OpenClaw, Hermes, or any repo with a workspace),
scaffold the bundled skills into it:

```bash
cd /path/to/agent/workspace
gbrain skillpack scaffold --all       # copy 43 curated skills + RESOLVER.md
```

Scaffolded skills are first-class files in your repo. Edit freely; re-running scaffold
refuses to overwrite anything that exists. Use `gbrain skillpack reference <name>` to
diff against gbrain's bundle when you want upstream improvements. (The legacy
`gbrain skillpack install` managed-block model was retired in v0.36.0.0 — run
`gbrain skillpack migrate-fence` once if upgrading from an older release.)

Whether you scaffolded or not, read `skills/RESOLVER.md` (in your workspace, or the
bundled copy at `~/gbrain/skills/RESOLVER.md` when running from the cloned repo). It's
the skill dispatcher — tells you which skill to read for any task. Save this to your
memory permanently.

The three most important skills to adopt immediately:

1. **Signal detector** (`skills/signal-detector/SKILL.md`) — fire this on EVERY
   inbound message. It captures ideas and entities in parallel. The brain compounds.

2. **Brain-ops** (`skills/brain-ops/SKILL.md`) — brain-first lookup on every response.
   Check the brain before any external API call.

3. **Conventions** (`skills/conventions/quality.md`) — citation format, back-linking
   iron law, source attribution. These are non-negotiable quality rules.

## Step 6: Identity (optional)

Run the soul-audit skill to customize the agent's identity:

```
Read skills/soul-audit/SKILL.md and follow it.
```

This generates SOUL.md (agent identity), USER.md (user profile), ACCESS_POLICY.md
(who sees what), and HEARTBEAT.md (operational cadence) from the user's answers.

If skipped, minimal defaults are installed automatically.

## Step 7: Recurring Jobs

Set up using your platform's scheduler (OpenClaw cron, Railway cron, crontab), or skip the
platform glue entirely with `gbrain autopilot --install` (built-in self-maintaining daemon):

- **Live sync** (every 15 min): `gbrain sync --repo ~/brain && gbrain embed --stale`
  — or `gbrain sync --watch` for a continuous loop.
- **Auto-update** (daily): `gbrain check-update --json` (tell user, never auto-install).
- **Dream cycle** (nightly): `gbrain dream` runs the 8-phase overnight maintenance cycle.
  Entity sweep, citation fixes, memory consolidation, plus (v0.23+) overnight conversation
  synthesis and cross-session pattern detection. One cron-friendly command. This is what
  makes the brain compound. Do not skip it. See `docs/guides/cron-schedule.md` for the
  full protocol.
- **Weekly**: `gbrain doctor --json && gbrain embed --stale`

## Step 8: Integrations

Run `gbrain integrations list`. Each recipe in `~/gbrain/recipes/` is a self-contained
installer. It tells you what credentials to ask for, how to validate, and what cron
to register. Ask the user which integrations they want (email, calendar, voice, Twitter).

Verify: `gbrain integrations doctor` (after at least one is configured)

## Step 9: Verify

Read `docs/GBRAIN_VERIFY.md` and run all 7 verification checks. Check #4 (live sync
actually works) is the most important.

## Upgrade

If you installed via `bun install -g`:

```bash
gbrain upgrade                        # self-updates the binary, runs schema migrations,
                                      # and prints post-upgrade notes for the version range
```

If you installed via `git clone + bun link`:

```bash
cd ~/gbrain && git pull origin master && bun install
gbrain apply-migrations --yes         # apply schema migrations (idempotent)
gbrain post-upgrade                   # show migration notes for the version range
```

Then read `~/gbrain/skills/migrations/v<NEW_VERSION>.md` (and any intermediate
versions you skipped) and run any backfill or verification steps it lists. Skipping
this is how features ship in the binary but stay dormant in the user's brain.

**v0.32.3 search modes (one-time upgrade prompt):** if the user's brain was
created before v0.32.3, `gbrain post-upgrade` prints a banner including the
9-cell cost matrix (mode × downstream model) preceded by `[AGENT]` markers.
**Do NOT silently move past the banner.** Present the matrix to the operator
verbatim, ask which mode they want (recommended default: `tokenmax` to preserve
v0.31.x retrieval shape), then run `gbrain config set search.mode <mode>`. See
Step 3.5 above for the full ask-the-user protocol — the upgrade path uses the
same matrix and same default.

For v0.12.0+ specifically: if your brain was created before v0.12.0, run
`gbrain extract links --source db && gbrain extract timeline --source db` to
backfill the new graph layer (see Step 4.5 above).

For v0.12.2+ specifically: if your brain is Postgres- or Supabase-backed and
predates v0.12.2, the `v0_12_2` migration runs `gbrain repair-jsonb`
automatically during `gbrain post-upgrade` to fix the double-encoded JSONB
columns. PGLite brains no-op. If wiki-style imports were truncated by the old
`splitBody` bug, run `gbrain sync --full` after upgrading to rebuild
`compiled_truth` from source markdown.

## v0.42.0+ onboard surface (NEW)

`gbrain onboard` is the activation surface gbrain did not have before.
Once your brain has any content, run `gbrain onboard --check --json` to
see structured recommendations across 5 brain-health axes (orphans,
stale embeddings, entity link coverage, timeline coverage, takes count).

**On first connect (after `gbrain init`):**
```bash
gbrain onboard --check --json
```
The JSON envelope (`schema_version: 1`) carries `recommendations[]` with
`apply_policy` per item: `auto_apply` (safe to run unattended),
`prompt_required` (needs explicit user consent), or `manual_only`
(LLM-bearing, user must run themselves).

**After every `gbrain upgrade`:**
```bash
gbrain onboard --check --json
```
New versions may surface new opportunities. The post-upgrade banner
nudges the user when it runs, but agents should re-probe as a hygiene
step regardless.

**Unattended remediation (cron / autopilot):**
```bash
gbrain onboard --auto --max-usd 5
```
Refuses without `--max-usd N`. Runs auto-eligible items only. The
autopilot daemon also consults onboard recommendations on its tick — no
explicit agent action needed for the autonomous path.

**Remote / federated brain installs (MCP):**
The `run_onboard` MCP op (admin scope) lets thin-client agents probe
brain health + drive remediation over OAuth-authenticated MCP. Protected
LLM-bearing handlers (synthesize, patterns, consolidate, takes-bootstrap,
contextual_reindex_per_chunk) require the additional `run_protected_onboard`
scope — admin alone is insufficient. The MCP op returns
`skipped_missing_scope[]` listing what would have run with the right
grants.

**Privacy + consent gates:**
- `gbrain takes extract --from-pages` sends concept/atom/lore/briefing/
  writing/originals page content to your configured chat model (default
  Anthropic Haiku). Refuses to run unless `takes.bootstrap_enabled=true`
  is set in config AND `--yes` is passed. Two-gate opt-in by design.
- Autopilot's auto-apply tier for takes-bootstrap stays `manual_only`
  until v0.42.1's eval gate (do not bypass).

**Suppress nudges in CI / scripted environments:**
```bash
export GBRAIN_NO_ONBOARD_NUDGE=1
```
Init + upgrade banners auto-skip in non-TTY too.

---

## skills/RESOLVER.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/skills/RESOLVER.md

# GBrain Skill Resolver

This is the dispatcher. Skills are the implementation. **Read the skill file before acting.** If two skills could match, read both. They are designed to chain (e.g., ingest then enrich for each entity).

## Always-on (every message)

| Trigger | Skill |
|---------|-------|
| Every inbound message (spawn parallel, don't block) | `skills/signal-detector/SKILL.md` |
| Any brain read/write/lookup/citation | `skills/brain-ops/SKILL.md` |

## Brain operations

| Trigger | Skill |
|---------|-------|
| "What do we know about", "tell me about", "search for", "who is", "background on", "notes on" | `skills/query/SKILL.md` |
| "Who knows who", "relationship between", "connections", "graph query" | `skills/query/SKILL.md` (use graph-query) |
| Creating/enriching a person or company page | `skills/enrich/SKILL.md` |
| Where does a new file go? Filing rules | `skills/repo-architecture/SKILL.md` |
| "where does this brain page go", "file this in the brain", "brain taxonomist", "taxonomy check", "refile brain page", "which directory does this page go" | `skills/brain-taxonomist/SKILL.md` |
| "EIIRP", "everything in its right place", "store this research", "put this in the brain", "make this re-doable", "DRY this up", "file all of this", "organize all of this work", "archive this research thread" | `skills/eiirp/SKILL.md` |
| Fix broken citations in brain pages | `skills/citation-fixer/SKILL.md` |
| "citation audit", "check citations", "fix citations" | `skills/citation-fixer/SKILL.md` (focused fix). For broader brain health, chain into `skills/maintain/SKILL.md` |
| "Research", "track", "extract from email", "investor updates", "donations" | `skills/data-research/SKILL.md` |
| Share a brain page as a link | `skills/publish/SKILL.md` |
| "validate frontmatter", "check frontmatter", "fix frontmatter", "frontmatter audit", "brain lint" | `skills/frontmatter-guard/SKILL.md` |
| "what search mode", "is my cache hot", "tune my retrieval", "compare search modes", "clear search overrides" | `gbrain search modes/stats/tune` directly. See `skills/conventions/search-modes.md` |
| "eval results", "search benchmark", "haters-immune methodology", "regression check on retrieval" | `gbrain eval run-all` / `gbrain eval compare`. See `docs/eval/SEARCH_MODE_METHODOLOGY.md` |

## Content & media ingestion

| Trigger | Skill |
|---------|-------|
| "capture this", "save this thought", "remember this", "drop this in the inbox", "save to brain" | `skills/capture/SKILL.md` |
| User shares a link, article, tweet, or idea | `skills/idea-ingest/SKILL.md` |
| "watch this video", "process this YouTube link", "ingest this PDF", "save this podcast", "process this book", "summarize this book", "PDF book", "ingest it into my brain", "what's in this screenshot", "check out this repo" | `skills/media-ingest/SKILL.md` |
| Meeting transcript received | `skills/meeting-ingestion/SKILL.md` |
| Generic "ingest this" (auto-routes to above) | `skills/ingest/SKILL.md` |

## Thinking skills (from GStack)

| Trigger | Skill |
|---------|-------|
| "Brainstorm", "I have an idea", "office hours" | GStack: office-hours |
| "Review this plan", "CEO review", "poke holes" | GStack: ceo-review |
| "Debug", "fix", "broken", "investigate" | GStack: investigate |
| "Retro", "what shipped", "retrospective" | GStack: retro |

> These skills come from GStack. If GStack is installed, the agent reads them directly.
> If not, brain-only mode still works (brain skills function without thinking skills).

## Operational

| Trigger | Skill |
|---------|-------|
| Task add/remove/complete/defer/review | `skills/daily-task-manager/SKILL.md` |
| Morning prep, meeting context, day planning | `skills/daily-task-prep/SKILL.md` |
| Daily briefing, "what's happening today" | `skills/briefing/SKILL.md` |
| Cron scheduling, quiet hours, job staggering | `skills/cron-scheduler/SKILL.md` |
| Save or load reports | `skills/reports/SKILL.md` |
| "Create a skill", "improve this skill" | `skills/skill-creator/SKILL.md` |
| "Skillify this", "is this a skill?", "make this proper" | `skills/skillify/SKILL.md` |
| "Compress my resolver", "AGENTS.md too large", "RESOLVER.md too big", "functional area dispatcher", "shrink routing table" | `skills/functional-area-resolver/SKILL.md` |
| "Is gbrain healthy?", morning health check, skillpack-check | `skills/skillpack-check/SKILL.md` |
| "harvest this skill into gbrain", "publish this skill to gbrain", "lift this skill upstream", "share this skill with other gbrain clients", "promote my skill to gbrain" | `skills/skillpack-harvest/SKILL.md` |
| Post-restart health + auto-fix, "did the container restart break anything", smoke test | `skills/smoke-test/SKILL.md` |
| Cross-modal review, second opinion | `skills/cross-modal-review/SKILL.md` |
| "Validate skills", skill health check | `skills/testing/SKILL.md` |
| Webhook setup, external event processing | `skills/webhook-transforms/SKILL.md` |
| "Spawn agent", "background task", "parallel tasks", "steer agent", "pause/resume agent", "gbrain jobs submit", "submit a gbrain job", "submit a shell job", "shell job" | `skills/minion-orchestrator/SKILL.md` |
| "present options", "ask before proceeding", "choice gate", "user decision" | `skills/ask-user/SKILL.md` |

## Setup & migration

| Trigger | Skill |
|---------|-------|
| "Set up GBrain", first boot | `skills/setup/SKILL.md` |
| "Now what?", "fill my brain", "cold start", "bootstrap", "import my data", "what should I import first" | `skills/cold-start/SKILL.md` |
| "Migrate from Obsidian/Notion/Logseq" | `skills/migrate/SKILL.md` |
| Brain health check, maintenance run | `skills/maintain/SKILL.md` |
| "Extract links", "build link graph", "populate timeline" | `skills/maintain/SKILL.md` (extraction sections) |
| "Run dream", "process today's session", "synthesize my conversations", "consolidate yesterday's conversations", "what patterns did you see", "did the dream cycle run" | `skills/maintain/SKILL.md` (dream cycle section) |
| "Brain health", "what features am I missing", "brain score" | Run `gbrain features --json` |
| "Set up autopilot", "run brain maintenance", "keep brain updated" | Run `gbrain autopilot --install --repo ~/brain` |
| Agent identity, "who am I", customize agent | `skills/soul-audit/SKILL.md` |
| "Populate links", "extract links", "backfill graph" | `skills/maintain/SKILL.md` (graph population phase) |
| "Populate timeline", "extract timeline entries" | `skills/maintain/SKILL.md` (graph population phase) |

## Identity & access (always-on)

| Trigger | Skill |
|---------|-------|
| Non-owner sends a message | Check `ACCESS_POLICY.md` before responding |
| Agent needs to know its identity/vibe | Read `SOUL.md` |
| Agent needs user context | Read `USER.md` |
| Operational cadence (what to check and when) | Read `HEARTBEAT.md` |

## Disambiguation rules

When multiple skills could match:
1. Prefer the most specific skill (meeting-ingestion over ingest)
2. If the user mentions a URL, route by content type (link → idea-ingest, video → media-ingest)
3. If the user mentions a person/company, check if enrich or query fits better
4. Chaining is explicit in each skill's Phases section
5. When in doubt, ask the user (see `skills/ask-user/SKILL.md` for the choice-gate pattern)

## Conventions (cross-cutting)

These apply to ALL brain-writing skills:
- `skills/conventions/quality.md` — citations, back-links, notability gate
- `skills/conventions/brain-first.md` — check brain before external APIs
- `skills/conventions/brain-routing.md` — which brain (DB) and which source (repo) to target; cross-brain federation is latent-space only
- `skills/conventions/schema-evolution.md` — when to add a type vs alias vs prefix (read before `schema-author`)
- `skills/conventions/subagent-routing.md` — when to use Minions vs inline work
- `skills/ask-user/SKILL.md` — choice-gate pattern for human input at decision points
- `skills/_brain-filing-rules.md` — where files go
- `skills/_output-rules.md` — output quality standards

## Uncategorized

| Trigger | Skill |
|---------|-------|
| "personalized version of this book", "mirror this book", "two-column book analysis", "apply this book to my life", "how does this book apply to me" | `skills/book-mirror/SKILL.md` |
| "enrich this article", "enrich brain pages", "batch enrich", "make brain pages useful" | `skills/article-enrichment/SKILL.md` |
| "strategic reading", "read this through the lens of", "apply this to my problem", "what can I learn from this about", "extract a playbook from" | `skills/strategic-reading/SKILL.md` |
| "concept synthesis", "synthesize my concepts", "find patterns across my notes", "build my intellectual map", "trace idea evolution" | `skills/concept-synthesis/SKILL.md` |
| "perplexity research", "what's new about", "current state of", "web research", "what changed about" | `skills/perplexity-research/SKILL.md` |
| "crawl my archive", "find gold in my archive", "archive crawler", "scan my dropbox for", "mine my old files for" | `skills/archive-crawler/SKILL.md` |
| "verify this academic claim", "check this study", "academic verify", "validate citation", "is this study real" | `skills/academic-verify/SKILL.md` |
| "make pdf from brain", "brain pdf", "convert brain page to pdf", "publish this page as pdf", "export brain page" | `skills/brain-pdf/SKILL.md` |
| "voice note", "ingest this voice memo", "transcribe and file", "voice note ingest", "save this audio note" | `skills/voice-note-ingest/SKILL.md` |
| "add a page type", "add a type to my schema", "schema author", "schema mutate", "schema pack add", "my brain has untyped pages", "propose new types from my corpus", "backfill page types", "evolve my schema", "researcher type", "make X an expert type" (dispatcher for: gbrain schema active/list/show/validate/graph/lint/stats/explain/use/downgrade/reload/init/fork/edit/diff/add-type/remove-type/update-type/add-alias/remove-alias/add-prefix/remove-prefix/add-link-type/remove-link-type/set-extractable/set-expert-routing/detect/suggest/review-candidates/review-orphans/sync) | `skills/schema-author/SKILL.md` |
| "unify my types", "migrate to gbrain-base-v2", "94 types to 14", "apply canonical taxonomy", "clean up my page types", "pack upgrade", "shrink type proliferation", "consolidate page types", "retype pages to canonical" (dispatcher for: gbrain onboard --check, gbrain onboard --check --explain, gbrain jobs submit unify-types, gbrain pages restore) | `skills/schema-unify/SKILL.md` |

---

## README.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/README.md

# GBrain

**Search gives you raw pages. GBrain gives you the answer.** It's the brain layer your AI agent has been missing — the only one that does synthesis, graph traversal, and gap analysis in one box.

I'm Garry Tan, President and CEO of Y Combinator. I built GBrain to run my own AI agents. It's the production brain behind my OpenClaw and Hermes deployments: **146,646 pages, 24,585 people, 5,339 companies**, 66 cron jobs running autonomously. My agent ingests meetings, emails, tweets, voice calls, and original ideas while I sleep. It enriches every person and company it encounters. It fixes its own citations and consolidates memory overnight. I wake up smarter than when I went to bed — and so will you.

**And now it works as a company brain too.** Each person on the team gets their own slice of the brain, scoped by login. When you query, you only see what you're allowed to see — never another person's notes, never another team's data. We fuzz-tested this across every way you can read the brain (search, list, lookup, multi-source reads) and got zero leaks. Drop GBrain in as your team's shared institutional memory — the [company-brain](https://www.ycombinator.com/rfs#company-brain) shape YC just put on its Request for Startups. If you're building in that space, you might as well build on this. **[Tutorial: set up GBrain as your company brain →](docs/tutorials/company-brain.md)**

Lots of personal-knowledge systems give you keyword matching and grep in a box. GBrain does that, and adds two things nobody else ships together:

- **A synthesis layer that gives you the actual answer.** Synthesized, well-cited prose across people, companies, deals, and ideas. Not "here are 10 chunks that mention your query"; an actual answer with citations and an explicit note on what the brain doesn't know yet. The gap analysis is the part that changes how you use the brain.
- **A self-wiring knowledge graph.** Every page write extracts entity refs and creates typed edges (`attended`, `works_at`, `invested_in`, `founded`, `advises`) with zero LLM calls. Ask "who works at Acme AI?" or "what did Bob invest in this quarter?" and get answers vector search alone can't reach. Benchmarked: **P@5 49.1%, R@5 97.9%** on a 240-page Opus-generated rich-prose corpus, **+31.4 points P@5** over its graph-disabled variant and over ripgrep-BM25 + vector-only RAG by a similar margin. Full BrainBench scorecards live in the sibling [gbrain-evals](https://github.com/garrytan/gbrain-evals) repo.

The point of building a 100K-page brain is to use it as a strategic moat. To never lose context. To query what's in your own head without re-reading it. The brain layer is what makes the moat usable. The 24/7 dream cycle is what keeps it sharp. Both run on your hardware, your DB, your keys.

It's easier to ship a daemon that runs 24/7 to ingest, enrich, and consolidate than it is to keep an agent in chat working hard. GBrain is that daemon, generalized. Install in 30 minutes. Your agent does the work. As my personal agent gets smarter, so does yours.

> **~30 minutes to a fully working brain.** Database ready in 2 seconds (PGLite, no server). You just answer questions about API keys.

> **LLMs:** fetch [`llms.txt`](llms.txt) for the documentation map, or [`llms-full.txt`](llms-full.txt) for the same map with core docs inlined in one fetch. **Agents:** start with [`AGENTS.md`](AGENTS.md) (or [`CLAUDE.md`](CLAUDE.md) if you're Claude Code).

## What this looks like

Say you have a meeting with Alice tomorrow. You want to walk in remembering what she works on, when you last talked, and what's still open between you. Here's what you'd type, and what you'd get back.

**You ask:**

> "What do I need to know before my meeting with Alice tomorrow?"

**Most personal-knowledge tools give you back a list of pages.** Something like:

```
1. people/alice — Alice runs engineering at Acme...
2. meetings/2026-03-15-alice-q1 — Q1 product review with Alice...
3. meetings/2026-01-08-acme-kickoff — Kickoff meeting with Acme team...
4. customers/acme — Acme is a series-B fintech we work with...
5. notes/2026-04-22 — Quick chat with Alice about pricing...
```

Five pages you now have to open and read yourself to actually prepare. The tool found the right material, but it didn't do the work.

**GBrain gives you back the answer, with sources:**

```
Alice runs engineering at Acme (a series-B fintech). You last spoke
on April 22 in a quick pricing chat. Three things are still open
from that conversation:

1. She owes you the security review for the new tier
   (deadline was May 1; no update since).
2. You committed to pricing for a 500-seat tier
   (you sent it April 25; no response yet).
3. She mentioned they're hiring a CISO; you said you'd intro
   someone from your network.

Heads up: nothing's been added to the brain about Alice or Acme
since April 22, six weeks ago. She may have replied through email
or Slack DM, channels the brain doesn't see. Worth asking her to
catch up before assuming any of this is still current.
```

Every claim has a source page behind it. The "heads up" at the end tells you what the brain doesn't know yet, so you can ask Alice about it directly instead of being surprised. The brain just did your meeting prep.

This is the difference between a search engine and a brain. Search finds the pages. The brain reads them for you and writes the answer.

## Install

GBrain is designed to be installed and operated by an AI agent. The fastest path is to have your agent do it for you. The CLI and MCP paths below are for people who want to wire it up themselves.

### Have your agent install it (recommended)

If you don't already have an AI agent platform running, start with one of these. Both are designed to read GBrain's install protocol and execute it:

- **[OpenClaw](https://github.com/openclawagents/openclaw)** — deploy [AlphaClaw on Render](https://render.com/deploy?repo=https://github.com/chrysb/alphaclaw) (one click, 8GB+ RAM)
- **[Hermes](https://github.com/openclawagents/hermes)** — deploy on [Railway](https://github.com/praveen-ks-2001/hermes-agent-template) (one click)

Then paste this into your agent:

```
Retrieve and follow the instructions at:
https://raw.githubusercontent.com/garrytan/gbrain/master/INSTALL_FOR_AGENTS.md
```

The agent installs GBrain, creates the brain, asks for your API keys, loads 43 skills, configures the dream cycle, and verifies the install end-to-end. ~30 minutes. You answer questions, it does the work.

> **Never set up an AI agent platform before?** The [personal-brain tutorial](docs/tutorials/personal-brain.md) walks the whole path end-to-end — picking OpenClaw vs Hermes, deploying it, pointing it at INSTALL_FOR_AGENTS.md, getting the API keys, and verifying the first query. Start there if any of the above is new.

### Install it into your existing agent

Already running Codex, Claude Code, Cursor, or another coding agent? Paste the same instruction in:

```
Retrieve and follow the instructions at:
https://raw.githubusercontent.com/garrytan/gbrain/master/INSTALL_FOR_AGENTS.md
```

This works in any agent that can read files over HTTPS and execute shell commands. Tested with Codex, Claude Code, Claude Cowork, Cursor, and AlphaClaw.

### CLI standalone (no agent)

```bash
bun install -g github:garrytan/gbrain
gbrain init --pglite     # 2 seconds; no server, no Docker
gbrain doctor            # verify health
gbrain import ~/notes/   # index your markdown
gbrain query "what themes show up across my notes?"
```

Postgres-at-scale, Supabase, and thin-client setup paths live in [`docs/INSTALL.md`](docs/INSTALL.md).

### Connect GBrain to your AI client (MCP)

GBrain exposes 30+ tools over MCP (stdio and HTTP). The specific snippet depends on which client you use:

- **[Claude Code](docs/mcp/CLAUDE_CODE.md)** — one command: `claude mcp add gbrain -- gbrain serve`. Zero server, zero tunnel.
- **[Cursor / Windsurf / any stdio MCP client](docs/mcp/CLAUDE_CODE.md)** — same shape, add `{"command": "gbrain", "args": ["serve"]}` to your MCP config.
- **[Claude Desktop (Cowork)](docs/mcp/CLAUDE_DESKTOP.md)** — Settings → Integrations → add the URL of your HTTP server. Remote only; the local `claude_desktop_config.json` does not work for remote servers.
- **[Claude Cowork (team plan)](docs/mcp/CLAUDE_COWORK.md)** — org Owner adds the connector under Organization Settings → Connectors.
- **[Perplexity Computer](docs/mcp/PERPLEXITY.md)** — Settings → Connectors → add the URL + bearer token. Pro subscription required.
- **[ChatGPT](docs/mcp/CHATGPT.md)** — uses OAuth 2.1 with PKCE (the hard requirement). Register a `chatgpt` client from the admin dashboard with grant type `authorization_code`.

For the HTTP server itself:

```bash
gbrain serve              # stdio MCP (local subprocess; for Claude Code, Cursor, Windsurf)
gbrain serve --http       # HTTP MCP with OAuth 2.1 + admin dashboard at /admin
                          # (required for Claude Desktop, Cowork, Perplexity, ChatGPT)
```

The HTTP server includes DCR-style client registration, scope-gated access (`read` / `write` / `admin`), and rate limiting. Deployment guides (ngrok, Railway, Fly.io) live under [`docs/mcp/`](docs/mcp/).

## Two ways to query your brain

Raw retrieval (what most personal-knowledge tools ship) and a synthesis layer that gives you an actual answer. They serve different jobs.

```bash
# raw retrieval: top pages by hybrid score, fast, no LLM cost
gbrain search "who's working on AI agents at portfolio companies?"

# brain layer: synthesized answer with citations and gap analysis
gbrain think "who's working on AI agents at portfolio companies?"
```

**`gbrain search`** returns the top retrieved pages, ranked by hybrid scoring (vector + keyword + RRF + source-tier boost + reranker). Use it when you want raw material to skim: agent context windows, citation lookups, finding a specific quote.

**`gbrain think`** runs the same retrieval, then composes a synthesized answer across the results with explicit citations to the source pages AND an honest note on what the brain doesn't know yet. The gap analysis is the differentiator: the answer tells you when a page is stale, when a claim is uncited, when two pages contradict each other, when there's a hole you should fill.

**Why it compounds.** Pair the brain layer with `find_trajectory` and you get answers like *"how have the company's metrics changed AND what does the team look like right now AND what did they promise / share AND when did we last meet AND what's the value-add I can offer here"*: well-scored, well-cited, in one shot. That's the strategic moat. That's why building a 100K-page brain is worth the effort.

`gbrain agent run "..."` exposes the same surface to a sub-agent through the Minions queue, with crash-safe two-phase persistence. Same answers, durable.

## How to get data in

One command, local or hosted, synchronous receipt:

```bash
gbrain capture "the thought I want to remember"
gbrain capture --file ./notes/today.md
echo "from a pipe" | gbrain capture --stdin
SLUG=$(gbrain capture "..." --quiet)
```

The page lands in the database and on disk in one move. Default slug `inbox/YYYY-MM-DD-<hash8>` so captures cluster in a predictable triage location. On thin-client installs the verb routes through MCP to the server: same command, same UX.

For webhook ingestion (Zapier / IFTTT / Apple Shortcuts):

```bash
curl -X POST https://your-brain/ingest \
  -H "Authorization: Bearer $TOKEN" \
  -H "Content-Type: text/markdown" \
  -d "# a thought from a Shortcut"
```

For mobile capture, the inbox folder source picks up anything dropped into
`~/.gbrain/inbox/` from iOS Shortcuts / AirDrop / Drafts / Finder.

Third-party skillpacks can ship custom ingestion sources (Granola, Linear,
voice, OCR) against the versioned `IngestionSource` contract at
`gbrain/ingestion`. See [`docs/skillpack-anatomy.md`](docs/skillpack-anatomy.md).

## Your brain's shape (schema packs)

Most personal-knowledge tools force one fixed layout: their idea of "notes" + "people" + "tags." Drop a Notion export or your own years-old Obsidian vault on top, and the agent doesn't know what a `Projects/` folder means or whether `Reading/` is people or sources.

**gbrain doesn't have a fixed layout.** It ships with bundled schema packs and lets you author your own when none fit:

- **`gbrain-base-v2`** (default as of v0.41.22) — 15-type DRY/MECE canonical taxonomy (14 canonical + `note` catch-all): `person`, `company`, `media`, `tweet`, `social-digest`, `analysis`, `atom`, `concept`, `source`, `deal`, `email`, `slack`, `writing`, `project`, `note`. Subtypes/format/origin pushed to frontmatter. The taxonomy that responds to issue #1479.
- **`gbrain-base`** (legacy, v0.41 and earlier brains) — the original 24-type layout. Stays bundled for back-compat; brains on it can upgrade via `gbrain onboard --check --explain` → `gbrain jobs submit unify-types --allow-protected --params '{"target_pack":"gbrain-base-v2"}'`.
- **`gbrain-recommended`** — extends `gbrain-base` with the 13 additional directories from `docs/GBRAIN_RECOMMENDED_SCHEMA.md` (source, place, trip, conversation, personal, civic, project, etc.). Activate with `gbrain schema use gbrain-recommended`.
- **Your own pack** — `gbrain schema detect` clusters your actual filesystem into proposed types, `gbrain schema suggest` runs an LLM pass over them, and `gbrain schema review-candidates --apply` promotes the ones you like. Three commands and the brain knows your shape. Authoring a successor pack (declares `migration_from:` so existing brains can opt in): see [`docs/architecture/pack-upgrade-mechanism.md`](docs/architecture/pack-upgrade-mechanism.md).

```bash
gbrain schema active                # which pack is running, which tier set it
gbrain schema list                  # bundled + installed packs
gbrain schema detect                # propose types matching your filesystem
gbrain schema suggest               # LLM-refined proposals on top of detect
gbrain schema review-candidates     # human gate: promote / rename / ignore
gbrain schema use my-pack           # activate
```

The active pack threads through every read + write path: `parseMarkdown` infers page type from the pack's path prefixes; `whoknows` scopes expert routing to types declared `expert_routing: true`; `extract_facts` runs only on `extractable: true` types; the search cache folds the pack name + version into its key so cross-pack contamination is structurally impossible. Switch packs and the brain re-interprets itself; switch back and nothing's lost.

Seven-tier resolution chain (per-call flag → env var → per-source DB key → brain-wide DB key → `gbrain.yml` → `~/.gbrain/config.json` → `gbrain-base` default). Full reference + authoring guide: [`docs/architecture/schema-packs.md`](docs/architecture/schema-packs.md).

## Tutorials

Step-by-step walkthroughs for getting the most out of GBrain. Each one takes you from zero to a working outcome, with concrete commands and real numbers.

- [**Set up your personal AI agent + brain from zero**](docs/tutorials/personal-brain.md) — the canonical full-stack install. Two GitHub repos, a Telegram bot, AlphaClaw on Render, OpenClaw + GBrain + Supabase. End-to-end in about 2 hours.
- [**Set up GBrain as your company brain**](docs/tutorials/company-brain.md) — federated, multi-user, OAuth-scoped institutional memory for a 10-50 person team. About 90 minutes end-to-end.

More walkthroughs in progress: connecting an existing agent (Claude Code, Cursor, OpenClaw, Hermes) to a GBrain memory layer; setting up GBrain for VC dealflow with founder scorecards and meeting prep; migrating an existing Notion or Obsidian vault; indexing a codebase as a queryable code brain. Full tutorial index: [`docs/tutorials/`](docs/tutorials/).

Want to see a tutorial that isn't here yet? [Open an issue](https://github.com/garrytan/gbrain/issues) describing the workflow you want documented.

## What it does (the loop)

```
  signal   →   search   →   respond   →   write   →   auto-link   →   sync
  (every    (brain-first  (informed     (page +    (typed edges     (cron
  message)  retrieval)    by context)   timeline)  + backlinks)     keeps fresh)
```

- **Signal detector** runs on every message your agent receives. Captures ideas, entity mentions, time-sensitive todos, names, links.
- **Brain-first lookup** before any external API call. The cheapest, fastest, most personal information source you have.
- **Auto-link** fires on every page write. No LLM calls; pure pattern matching on `[[wiki/people/bob]]` style references. New entity → new page stub → graph grows.
- **Cron-driven enrichment** runs while you sleep: dedup people pages, fix citations, score salience, find contradictions, prep tomorrow's tasks.

The whole loop is described in [`docs/architecture/topologies.md`](docs/architecture/topologies.md) with diagrams.

## Capabilities

**Hybrid search.** Vector (HNSW on pgvector) + BM25 keyword + reciprocal-rank fusion + source-tier boost + intent-aware query rewriting. Three named search modes (`conservative`, `balanced`, `tokenmax`) bundle the cost/quality knobs into a single config key. Live cost/recall comparisons in [`docs/eval/SEARCH_MODE_METHODOLOGY.md`](docs/eval/SEARCH_MODE_METHODOLOGY.md). Default: `balanced` with ZeroEntropy reranker on. Per-query graph signals notice when a top result is a hub for THAT query (adjacency boost), is corroborated across team brains (cross-source boost), or is being crowded out by weak chunks from a chatty session (session demote). Run `gbrain search "<query>" --explain` to see per-stage attribution: base score, every boost that fired, what it multiplied. `gbrain doctor` ships a `graph_signals_coverage` check; `gbrain search stats` shows fire counts and failure breakdowns. Vector retrieval pools the best chunk per page, so a page surfaces on its strongest evidence instead of losing to a neighbor on one weak chunk. Queries that match a page's title phrase or a declared free-text alias (`gbrain reindex --aliases` backfills existing pages) get boosted to the page they name. Every result carries an `evidence` tag (why it matched) and a `create_safety` hint (`exists` / `probable` / `unknown`) so an agent decides whether a page already exists instead of guessing from a raw score. `gbrain search diagnose "<query>" --target <slug>` traces which retrieval layer surfaces (or misses) a page.

**Self-wiring knowledge graph.** Every `put_page` extracts entity refs from markdown/wikilinks/typed-link syntax and writes edges with zero LLM calls. Typed edges (`attended`, `works_at`, `invested_in`, `founded`, `advises`, `mentions`, …). Multi-hop traversal via `gbrain graph-query`. The graph is what produces the +31.4 P@5 lift over vector-only RAG.

**Job queue (Minions).** BullMQ-shaped, Postgres-native job queue. Durable subagents (LLM tool loops that survive crashes via two-phase pending→done persistence), shell jobs with audit, child jobs with cascading timeouts, rate leases for outbound providers, attachments via S3/Supabase storage. Replaces "spawn subagent as fire-and-forget Promise" with something that recovers from anything.

**43 curated skills.** Routing lives in [`skills/RESOLVER.md`](skills/RESOLVER.md). Covers signal capture, ingest (idea / media / meeting), enrichment, querying, brain ops, citation fixing, daily task management, cron scheduling, reports, voice, soul audit, skill creation, eval framework, and migrations. Skills are markdown files (tool-agnostic), packaged as a single skillpack the installer drops into your agent workspace.

**Eval framework.** `gbrain eval longmemeval` runs the public [LongMemEval](https://huggingface.co/datasets/xiaowu0162/longmemeval) benchmark against your hybrid retrieval. `gbrain eval export` + `gbrain eval replay` capture real queries and replay them against code changes (set `GBRAIN_CONTRIBUTOR_MODE=1`). `gbrain eval cross-modal` cross-checks an output against the task using three different-provider frontier models. `gbrain eval retrieval-quality` runs NamedThingBench, which hard-gates the named-thing retrieval families (title-substring, alias-synonym, generic-to-named, multi-chunk-dilution) so a regression in "find the page this query names" fails CI loudly. Full methodology in [`docs/eval/SEARCH_MODE_METHODOLOGY.md`](docs/eval/SEARCH_MODE_METHODOLOGY.md).

**Brain consistency.** `gbrain eval suspected-contradictions` samples retrieval pairs, layered date pre-filter, query-conditioned LLM judge, persistent cache. Surfaces conflicts between takes + facts the agent has written. Wired into the daily dream cycle.

**Agent-authored schema (v0.40.7.0).** Your brain has a shape — what page types exist (`person`, `meeting`, `paper`, `case`, `lab-result`), what they link to (`attended`, `authored`, `prescribed-by`), what facts get extracted automatically. The default ships with 22 universal types, but your brain's actual shape is not the default shape. Agents can now evolve that shape on your behalf via 14 `gbrain schema` CLI verbs + a batched MCP op (`schema_apply_mutations`, admin scope, NOT localOnly so remote agents reach it over HTTPS). Atomic file locks, audit log with the agent's identity, chunked UPDATE backfill in 1000-row batches that never wedge concurrent writers. The brain stops being a pile of notes and becomes something with structure. **Why it matters:** [`docs/what-schemas-unlock.md`](docs/what-schemas-unlock.md) — 7 killer use cases (4000 invisible meetings, founder ops brain, research brain, legal brain, team brain, agent-as-co-curator). **5-minute walkthrough:** [`docs/schema-author-tutorial.md`](docs/schema-author-tutorial.md). **Agent skill:** [`skills/schema-author/SKILL.md`](skills/schema-author/SKILL.md).

## Integrations

Data flowing into the brain. Each integration is a recipe — markdown + setup hints — that ships in `recipes/` and is discoverable via `gbrain integrations list`.

- **Voice**: Phone calls create brain pages via Twilio + OpenAI Realtime (or DIY STT+LLM+TTS). Setup recipe: [`recipes/twilio-voice-brain.md`](recipes/twilio-voice-brain.md).
- **Email + calendar**: webhook handlers that route to brain signals. [`docs/integrations/meeting-webhooks.md`](docs/integrations/meeting-webhooks.md).
- **Embedding providers**: 16 recipes covering OpenAI (default fallback), OpenRouter, Voyage, ZeroEntropy (default), Google Gemini, Azure OpenAI, MiniMax, Alibaba DashScope, Zhipu, Ollama (local), llama.cpp llama-server (local), LiteLLM proxy. Pricing matrix + decision tree in [`docs/integrations/embedding-providers.md`](docs/integrations/embedding-providers.md).
- **Rerankers**: ZeroEntropy `zerank-2` hosted (default in `tokenmax` mode) plus the v0.40.6.1 `llama-server-reranker` recipe for fully-local cross-encoder rerank via llama.cpp — runs Qwen3-Reranker or self-hosted ZeroEntropy weights against the same `gateway.rerank()` seam. Setup walkthrough in [`docs/ai-providers/llama-server-reranker.md`](docs/ai-providers/llama-server-reranker.md).
- **Credential gateway**: vault-aware secret distribution. [`docs/integrations/credential-gateway.md`](docs/integrations/credential-gateway.md).
- **MCP clients**: every major MCP client is supported. [`docs/mcp/`](docs/mcp/) per-client setup.

## Architecture

**Two engines, one contract.** PGLite (Postgres 17 via WASM, zero-config, default) for personal brains up to ~50K pages. Postgres + pgvector (Supabase or self-hosted) for shared / large / multi-machine deployments. The contract-first `BrainEngine` interface in [`src/core/engine.ts`](src/core/engine.ts) defines ~47 operations both engines implement; CLI and MCP server are generated from one source.

**Brain repo is the system of record.** Your knowledge lives in a regular git repo (your "brain repo") as markdown files. GBrain syncs the repo into Postgres for retrieval; deletes in git become soft-deletes in DB. You can publish public subsets, share team mounts, run thin-client setups pointing at a colleague's brain server. Topologies in [`docs/architecture/topologies.md`](docs/architecture/topologies.md).

**Two organizational axes (brain ⊥ source).** A *brain* is a database (your personal brain, a team mount you joined). A *source* is a repo inside that brain (wiki, gstack, an essay, a knowledge base). Routing lives in `.gbrain-source` dotfiles and resolves via a documented 6-tier precedence chain. Full diagrams in [`docs/architecture/brains-and-sources.md`](docs/architecture/brains-and-sources.md).

**Why the graph matters.** Vector search returns chunks that are semantically close. The graph returns chunks that are factually connected. Hybrid search pulls from both; auto-linking on every write keeps the graph fresh. Deep dive: [`docs/architecture/RETRIEVAL.md`](docs/architecture/RETRIEVAL.md).

## Troubleshooting

**`gbrain import` fails with `expected N dimensions, not M`?** Run `gbrain doctor`. It will print the exact `gbrain config set ...` or `gbrain retrieval-upgrade` command to repair the mismatch. You should not need to delete `~/.gbrain`. Fresh `gbrain init --pglite` auto-detects your embedding provider from API keys in your environment: set `OPENAI_API_KEY` (or `ZEROENTROPY_API_KEY` / `VOYAGE_API_KEY`) before running init, or pass `--embedding-model <provider>:<model>` explicitly. With multiple keys set, init fires an interactive picker. In non-TTY contexts (CI, Docker) with no keys, init exits 1 with a paste-ready setup hint; pass `--no-embedding` to defer setup until runtime. See [`docs/integrations/embedding-providers.md`](docs/integrations/embedding-providers.md) for the full provider matrix and [`docs/operations/headless-install.md`](docs/operations/headless-install.md) for Docker/CI sequencing.

**Hourly cron sync keeps timing out on a federated brain?** v0.41.13.0 ships
two flags + a recommended pattern. Switch your cron to a per-source loop
with shell `timeout(1)` doing the OS-level kill and gbrain self-terminating
gracefully half-a-minute earlier:

```bash
gbrain sync --break-lock --all --max-age 1800
for src in $(gbrain sources list --json | jq -r '.[].id'); do
  timeout 600 gbrain sync --source "$src" --timeout 540 || true
done
```

When `--timeout` fires mid-import, `gbrain sync` exits 0 with status
`partial` and `last_commit` UNCHANGED — the next run re-walks the same
diff and `content_hash` short-circuits already-imported files. The
`--max-age 1800` first command self-heals any wedged-but-alive locks
left by a hung previous run, using the v98 `last_refreshed_at` semantic
(NOT `acquired_at`) so healthy long-running holders are safe by
construction. See the v0.41.13.0 entry in [`CHANGELOG.md`](CHANGELOG.md)
for the honest scope notes (extract + embed phases run to completion;
30-min rollout window for `--max-age` post-migration v98; full-sync
triggers deferred to v0.42+).

**Dream cycle silently losing wiki links on Supabase?** v0.41.19.0 fixes
the bug class structurally. The engine now self-retries every bulk batch
write (`addLinksBatch` / `addTimelineEntriesBatch` / `upsertChunks`) on
Supavisor pooler blips, with a 12s worst-case wait that covers the full
5-10s circuit-breaker recovery window. `gbrain doctor` surfaces incidents
via the new `batch_retry_health` check (reads the last 24h of
`~/.gbrain/audit/batch-retry-YYYY-Www.jsonl`). To tune for an unusually
slow pooler:

```bash
# Defaults: 3 retries, base 1s, max 10s, decorrelated jitter.
# Override per operator without a release:
export GBRAIN_BULK_MAX_RETRIES=5       # int >= 0; 0 disables retries
export GBRAIN_BULK_RETRY_BASE_MS=2000  # int > 0
export GBRAIN_BULK_RETRY_MAX_MS=15000  # int >= base
```

Bad values surface at `gbrain doctor` startup with a paste-ready fix
(not at first-retry mid-cycle). PGLite-only installs pay zero cost — the
retry wrap is engine-level, but PGLite has no pooler so retries never
fire in practice.

**Dream cycle losing ~150 link rows per run with `'No database
connection: connect() has not been called'` errors in the log?** v0.41.27.0
makes the retry layer self-heal on a nulled-out database singleton. A
new `reconnect` callback on `withRetry` rebuilds the connection between
attempts; `PostgresEngine.batchRetry` injects `() => this.reconnect()`
so engine-level batch writes survive a mid-cycle disconnect by something
else in the same process. Same release: `gbrain capture` no longer trails
a `'No database connection'` stderr line from a background facts:absorb
worker firing after CLI exit — the op-dispatch finally block awaits
`getFactsQueue().drainPending({timeout: 1000})` before
`engine.disconnect()`. To find which code path is still calling
disconnect mid-process, run `gbrain doctor --json | jq '.checks[] |
select(.id=="batch_retry_health")'`; the extended check now surfaces
24h disconnect-call count and the most-recent caller frame from a new
`~/.gbrain/audit/db-disconnect-YYYY-Www.jsonl` audit. (Closes #1570.)

**`gbrain brainstorm` returning `judge_failed: true` with 0 scored
ideas?** v0.41.21.0 closes the two bugs that caused it. The judge
hard-coded a 4K-token output cap; for any run past ~40 ideas the call
truncated mid-JSON and the parser threw. Same release closes a slash-
form pricing miss: `gbrain brainstorm --judge-model
anthropic/claude-sonnet-4-6 --max-cost 5` failed with
`BudgetExhausted reason=no_pricing` because every pricing site only
matched the colon form. Both shapes work now. No config change, no
schema migration — `gbrain upgrade` is the whole fix.

**`gbrain reindex --markdown` wiped your auto/dream/signal-detector
tags?** v0.41.37.0 makes tag reconciliation add-only. Re-import and
`reindex --markdown` now ADD current frontmatter tags and never delete,
so enrichment tags written to the DB (auto-tag, dream synthesize,
signal-detector) survive a re-chunk. The reindex DB-only fallback also
reconstructs the full markdown (frontmatter + body + timeline) before
re-chunking, so a page with no on-disk source keeps its frontmatter,
title, and timeline instead of getting overwritten with empty
frontmatter. Trade-off: removing a tag from a page's frontmatter no
longer removes it from the DB on the next sync (frontmatter-tag removal
needs a provenance column, deferred). (Closes #1621.)

**`gbrain sync` wedges on a large brain (no progress, high CPU)?**
v0.41.37.0 ships three things. First, name the stalling file:

```bash
GBRAIN_SYNC_TRACE=1 gbrain sync --no-pull --no-embed --yes
```

The last `[sync] begin import: <path>` line with no following completion
is the file being processed when the hang hit. Second, if you suspect a
schema-pack `inference.regex` with catastrophic backtracking, complete
the sync with the pack disabled and re-run extraction later:

```bash
gbrain sync --no-schema-pack --no-pull --no-embed --yes
```

`gbrain schema lint` now warns on the classic nested-quantifier ReDoS
shapes (`(a+)+`, `(a*)*`, …) in pack regexes, and the runtime caps
inference-regex input length (override via `GBRAIN_MAX_REGEX_INPUT_CHARS`).
Third, on a PGLite brain, stop `gbrain serve` before a large sync —
PGLite is single-writer and a live MCP server contends for the write
lock. See [`docs/architecture/serve-sync-concurrency.md`](docs/architecture/serve-sync-concurrency.md)
for the full triage. (Closes #1569.)

**`gbrain init --migrate-only` / a schema migration fails on Windows
with `getaddrinfo ENOTFOUND`?** v0.41.37.0 runs the 9 schema-bring-up
phases in-process instead of spawning a child `gbrain init
--migrate-only` per phase. The spawned child died on
Windows + bun + Supabase pooler with a DNS-resolution failure even
though the parent connected fine; running in-process removes the spawn
entirely. The v0.13.1 grandfather migration that hung 70+ minutes on an
82K-page PGLite brain is also fixed — it now runs as a chunked bulk SQL
pass (keyed on the page PK, soft-delete-filtered, source-safe) that
completes in ~1-2 seconds. (Closes #1605, #1581.)

## Docs

- [`docs/INSTALL.md`](docs/INSTALL.md) — every install path, end to end
- [`docs/what-schemas-unlock.md`](docs/what-schemas-unlock.md) — why schemas matter: 7 killer use cases, the structural argument for typed page kinds, the agent-co-curates pattern (v0.40.7.0)
- [`docs/schema-author-tutorial.md`](docs/schema-author-tutorial.md) — 5-minute walkthrough: fork the bundled pack, add a custom type, backfill existing pages, prove the wiring via `gbrain whoknows`
- [`docs/architecture/`](docs/architecture/) — system design, topologies, retrieval theory
- [`docs/guides/`](docs/guides/) — how-to runbooks (sub-agent routing, minion deployment, skill development, brain-first lookup, idea capture, diligence ingestion)
- [`docs/integrations/`](docs/integrations/) — connecting external data sources (voice, email, calendar, embedding providers)
- [`docs/mcp/`](docs/mcp/) — per-client MCP setup (Claude Desktop, Code, Cursor, ChatGPT, Perplexity, Cowork)
- [`docs/eval/`](docs/eval/) — eval framework, metric glossary, methodology
- [`docs/ethos/`](docs/ethos/) — philosophy (thin harness, fat skills, markdown as recipes, origin story)
- [`AGENTS.md`](AGENTS.md) — entry point for non-Claude agents
- [`CLAUDE.md`](CLAUDE.md) — entry point for Claude Code (deep operating context)
- [`CONTRIBUTING.md`](CONTRIBUTING.md) — contributor guide, test discipline, eval-capture mode
- [`SECURITY.md`](SECURITY.md) — OAuth threat model, hardening defaults

## Contributing

Run `bun run test` for the fast loop, `bun run verify` for the pre-push gate, `bun run ci:local` to run the full Docker-backed CI stack locally. Detailed test discipline in [`CONTRIBUTING.md`](CONTRIBUTING.md).

Community PRs are batched into release waves rather than merged one-by-one — see the "PR wave workflow" section in [`CLAUDE.md`](CLAUDE.md). Contributor attribution stays attached via `Co-Authored-By:` trailers. We credit every accepted contribution in [`CHANGELOG.md`](CHANGELOG.md).

If you find a bug or want a feature: open an issue first. Quick fixes (typo, doc bug, obvious regression) can go straight to a PR. Anything touching schema, retrieval ranking, MCP protocol, or the security boundary needs a design discussion in the issue first.

## License + credit

MIT. I built GBrain to run my OpenClaw and Hermes deployments — the production brain behind my AI agents.

Origin story: [`docs/ethos/ORIGIN.md`](docs/ethos/ORIGIN.md).

Community PR contributors are credited in `CHANGELOG.md` per release. ZeroEntropy ([@zeroentropy](https://zeroentropy.dev)) for the embedding + reranker stack that ships as the default. Voyage AI for the asymmetric-encoding recipe template. Ramp Labs for the search quality improvements lineage.

---

# Configuration

## docs/ENGINES.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/ENGINES.md

# Pluggable Engine Architecture

## The idea

Every GBrain operation goes through `BrainEngine`. The engine is the contract between "what the brain can do" and "how it's stored." Swap the engine, keep everything else.

v0 shipped `PostgresEngine` backed by Supabase. v0.7 adds `PGLiteEngine` -- embedded Postgres 17.5 via WASM (@electric-sql/pglite), zero-config default. The interface is designed so a `DuckDBEngine`, `TursoEngine`, or any custom backend could slot in without touching the CLI, MCP server, skills, or any consumer code.

## Why this matters

Different users have different constraints:

| User | Needs | Best engine |
|------|-------|-------------|
| Getting started | Zero-config, no accounts, no server | PGLiteEngine (default since v0.7) |
| Power user (you) | World-class search, 7K+ pages, zero-ops | PostgresEngine + Supabase |
| Open source hacker | Single file, no server, git-friendly | PGLiteEngine |
| Team/enterprise | Multi-user, RLS, audit trail | PostgresEngine + self-hosted |
| Researcher | Analytics, bulk exports, embeddings | DuckDBEngine (someday) |
| Edge/mobile | Offline-first, sync later | PGLiteEngine + sync (someday) |

The engine interface means we don't have to choose. PGLite is the zero-friction default. Supabase is the production scale path. `gbrain migrate --to supabase/pglite` moves between them.

## The interface

```typescript
// src/core/engine.ts

export interface BrainEngine {
  // Lifecycle
  connect(config: EngineConfig): Promise<void>;
  disconnect(): Promise<void>;
  initSchema(): Promise<void>;
  transaction<T>(fn: (engine: BrainEngine) => Promise<T>): Promise<T>;

  // Pages CRUD
  getPage(slug: string): Promise<Page | null>;
  putPage(slug: string, page: PageInput): Promise<Page>;
  deletePage(slug: string): Promise<void>;
  listPages(filters: PageFilters): Promise<Page[]>;

  // Search
  searchKeyword(query: string, opts?: SearchOpts): Promise<SearchResult[]>;
  searchVector(embedding: Float32Array, opts?: SearchOpts): Promise<SearchResult[]>;

  // Chunks
  upsertChunks(slug: string, chunks: ChunkInput[]): Promise<void>;
  getChunks(slug: string): Promise<Chunk[]>;

  // Links
  addLink(from: string, to: string, context?: string, linkType?: string): Promise<void>;
  removeLink(from: string, to: string): Promise<void>;
  getLinks(slug: string): Promise<Link[]>;
  getBacklinks(slug: string): Promise<Link[]>;
  traverseGraph(slug: string, depth?: number): Promise<GraphNode[]>;

  // Tags
  addTag(slug: string, tag: string): Promise<void>;
  removeTag(slug: string, tag: string): Promise<void>;
  getTags(slug: string): Promise<string[]>;

  // Timeline
  addTimelineEntry(slug: string, entry: TimelineInput): Promise<void>;
  getTimeline(slug: string, opts?: TimelineOpts): Promise<TimelineEntry[]>;

  // Raw data
  putRawData(slug: string, source: string, data: object): Promise<void>;
  getRawData(slug: string, source?: string): Promise<RawData[]>;

  // Versions
  createVersion(slug: string): Promise<PageVersion>;
  getVersions(slug: string): Promise<PageVersion[]>;
  revertToVersion(slug: string, versionId: number): Promise<void>;

  // Stats + health
  getStats(): Promise<BrainStats>;
  getHealth(): Promise<BrainHealth>;

  // Ingest log
  logIngest(entry: IngestLogInput): Promise<void>;
  getIngestLog(opts?: IngestLogOpts): Promise<IngestLogEntry[]>;

  // Config
  getConfig(key: string): Promise<string | null>;
  setConfig(key: string, value: string): Promise<void>;

  // Migration + advanced (added v0.7)
  runMigration(sql: string): Promise<void>;
  getChunksWithEmbeddings(slug: string): Promise<ChunkWithEmbedding[]>;
}
```

### Key design choices

**Slug-based API, not ID-based.** Every method takes slugs, not numeric IDs. The engine resolves slugs to IDs internally. This keeps the interface portable... slugs are strings, IDs are database-specific.

**Embedding is NOT in the engine.** The engine stores embeddings and searches by vector, but it doesn't generate embeddings. `src/core/embedding.ts` handles that. This is intentional: embedding is an external API call (OpenAI), not a storage concern. All engines share the same embedding service.

**Chunking is NOT in the engine.** Same logic. `src/core/chunkers/` handles chunking. The engine stores and retrieves chunks. All engines share the same chunkers.

**Search returns `SearchResult[]`, not raw rows.** The engine is responsible for its own search implementation (tsvector vs FTS5, pgvector vs sqlite-vss) but must return a uniform result type. RRF fusion and dedup happen above the engine, in `src/core/search/hybrid.ts`.

**`traverseGraph` exists but is engine-specific.** Postgres uses recursive CTEs. SQLite would use a loop with depth tracking. The interface is the same: give me a slug and max depth, return the graph.

## How search works across engines

```
                        +-------------------+
                        |  hybrid.ts        |
                        |  (RRF fusion +    |
                        |   dedup, shared)  |
                        +--------+----------+
                                 |
                    +------------+------------+
                    |                         |
           +--------v--------+       +--------v--------+
           | engine.search   |       | engine.search   |
           |   Keyword()     |       |   Vector()      |
           +-----------------+       +-----------------+
                    |                         |
        +-----------+-----------+   +---------+---------+
        |                       |   |                   |
+-------v-------+  +-------v---+   +-------v---+  +----v--------+
| Postgres:     |  | PGLite:   |   | Postgres: |  | PGLite:     |
| tsvector +    |  | tsvector +|   | pgvector  |  | pgvector    |
| ts_rank +     |  | ts_rank   |   | HNSW      |  | HNSW        |
| websearch_to_ |  | (same SQL)|   | cosine    |  | cosine      |
| tsquery       |  |           |   |           |  | (same SQL)  |
+---------------+  +-----------+   +-----------+  +-------------+
```

RRF fusion, multi-query expansion, and 4-layer dedup are engine-agnostic. They operate on `SearchResult[]` arrays. Only the raw keyword and vector searches are engine-specific.

## PostgresEngine (v0, ships)

**Dependencies:** `postgres` (porsager/postgres), `pgvector`

**Postgres-specific features used:**
- `tsvector` + `GIN` index for full-text search with `ts_rank` weighting
- `pgvector` HNSW index for cosine similarity vector search
- `pg_trgm` + `GIN` for fuzzy slug resolution
- Recursive CTEs for graph traversal
- Trigger-based search_vector (spans pages + timeline_entries)
- JSONB for frontmatter with GIN index
- Connection pooling via Supabase Supavisor (port 6543)

**Hosting:** Supabase Pro ($25/mo). Zero-ops. Managed Postgres with pgvector built in.

**Why not self-hosted for v0:** The brain should be infrastructure agents use, not something you maintain. Self-hosted Postgres with Docker is a welcome community PR, but v0 optimizes for zero ops.

## PGLiteEngine (v0.7, ships)

**Dependencies:** `@electric-sql/pglite` (v0.4.4+)

**What it is:** Embedded Postgres 17.5 compiled to WASM via ElectricSQL's PGLite. Runs in-process, no server, no Docker, no accounts. Same SQL as PostgresEngine -- not a separate dialect. All 37 BrainEngine methods implemented.

**PGLite-specific details:**
- Uses `pglite-schema.ts` for DDL (pgvector extension, pg_trgm, triggers, indexes)
- Parameterized queries throughout (shared utilities in `src/core/utils.ts`)
- `hybridSearch` keyword-only fallback when `OPENAI_API_KEY` is not set
- Data stored at `~/.gbrain/brain.db` (configurable)
- pgvector HNSW index for cosine similarity vector search (same as Postgres)
- tsvector + ts_rank for full-text search (same as Postgres)
- pg_trgm for fuzzy slug resolution (same as Postgres)

**When to use PGLite vs Postgres:**

| Factor | PGLite | PostgresEngine + Supabase |
|--------|--------|--------------------------|
| Setup | `gbrain init` (zero-config) | Account + connection string |
| Scale | Good for < 1,000 files | Production-proven at 10K+ |
| Multi-device | Single machine only | Any device via remote MCP |
| Cost | Free | Supabase Pro ($25/mo) |
| Concurrency | Single process | Connection pooling |
| Backups | Manual (file copy) | Managed by Supabase |

**Migration:** `gbrain migrate --to supabase` exports everything (pages, chunks, embeddings, links, tags, timeline) and imports into Supabase. `gbrain migrate --to pglite` goes the other direction. Bidirectional, lossless.

## Adding a new engine

1. Create `src/core/<name>-engine.ts` implementing `BrainEngine`
2. Add to engine factory in `src/core/engine-factory.ts`:
   ```typescript
   export function createEngine(type: string): BrainEngine {
     switch (type) {
       case 'pglite': return new PGLiteEngine();
       case 'postgres': return new PostgresEngine();
       case 'myengine': return new MyEngine();
       default: throw new Error(`Unknown engine: ${type}`);
     }
   }
   ```
   The factory uses dynamic imports so engines are only loaded when selected.
3. Store engine type in `~/.gbrain/config.json`: `{ "engine": "myengine", ... }`
4. Add tests. The test suite should be engine-agnostic where possible... same test cases, different engine constructor.
5. Document in this file + add a design doc in `docs/`

### What you DON'T need to touch

- `src/cli.ts` (dispatches to engine, doesn't know which one)
- `src/mcp/server.ts` (same)
- `src/core/chunkers/*` (shared across engines)
- `src/core/embedding.ts` (shared across engines)
- `src/core/search/hybrid.ts`, `expansion.ts`, `dedup.ts` (shared, operate on SearchResult[])
- `skills/*` (fat markdown, engine-agnostic)

### What you DO need to implement

Every method in `BrainEngine`. The full interface. No optional methods, no feature flags. If your engine can't do vector search (e.g., a pure-text engine), implement `searchVector` to return `[]` and document the limitation.

## Capability matrix

| Capability | PostgresEngine | PGLiteEngine | Notes |
|-----------|---------------|-------------|-------|
| CRUD | Full | Full | Same SQL |
| Keyword search | tsvector + ts_rank | tsvector + ts_rank | Identical (real Postgres) |
| Vector search | pgvector HNSW | pgvector HNSW | Identical (real Postgres) |
| Fuzzy slug | pg_trgm | pg_trgm | Identical (real Postgres) |
| Graph traversal | Recursive CTE | Recursive CTE | Same SQL |
| Transactions | Full ACID | Full ACID | Both support this |
| JSONB queries | GIN index | GIN index | Identical |
| Concurrent access | Connection pooling | Single process | PGLite limitation |
| Hosting | Supabase, self-hosted, Docker | Local file | |
| Migration methods | runMigration, getChunksWithEmbeddings | Same | Added v0.7 |

## Future engine ideas

**TursoEngine.** libSQL (SQLite fork) with embedded replicas and HTTP edge access. Would give SQLite's simplicity with cloud sync. Interesting for mobile/edge use cases.

**DuckDBEngine.** Analytical workloads. Bulk exports, embedding analysis, brain-wide statistics. Not for OLTP. Could be a secondary engine for analytics alongside Postgres for operations.

**Custom/Remote.** The interface is clean enough that someone could build an engine backed by any storage: Firestore, DynamoDB, a REST API, even a flat file system. The interface doesn't assume SQL.

Note: The original SQLite engine plan (`docs/SQLITE_ENGINE.md`) was superseded by PGLite. PGLite uses the same SQL as Postgres, eliminating the need for a separate SQLite dialect with FTS5/sqlite-vss translation.

---

## docs/what-schemas-unlock.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/what-schemas-unlock.md

# What schemas unlock

Most note-taking apps treat every page the same. You write something, it goes in a pile, you search the pile with text matching. Tags help, but tags are flat. After a few thousand pages, the pile gets noisy and the search gets stupid.

Schemas are how gbrain stops being a pile of notes and becomes something with structure. A schema declares what KINDS of things live in your brain (`person`, `company`, `meeting`, `researcher`, `case`, `lab-result`), what they link to (`attended`, `authored`, `prescribed-by`), what facts the system should extract automatically (`mrr=50000`, `damages=5000000`), and which types route through expert search vs general search.

The default schema (`gbrain-base`) ships with 22 page types covering the universal shapes — people, companies, meetings, notes, daily, calendar events. That's enough to start. But your brain is yours, and your brain's shape is not the default shape. A research brain needs `researcher` and `paper` as first-class types. A founder brain needs `lead`, `investor`, `portco`, `deal-stage`. A lawyer brain needs `case`, `motion`, `deposition`, `precedent`. Same engine, totally different shape.

v0.40.7.0 made it possible for AGENTS to author that shape for you. Not just "the user manually edits YAML in `~/.gbrain/schema-packs/mine/pack.yaml`" but "your agent sees the corpus, proposes a type, asks for approval, applies it atomically with a full audit trail, then backfills 4000 existing pages with one chunked SQL command." That's the new thing.

This doc is the WHY. The [tutorial](schema-author-tutorial.md) is the HOW.

## Killer use cases

### 1. The 4000 invisible pages

You have 4000 markdown files under `meetings/` going back two years. The default schema doesn't have a `meeting` type, so all 4000 are typed `note` (the catchall). When you run:

```bash
gbrain whoknows "Q3 roadmap discussion"
```

You get the top 10 text matches, ranked by raw relevance. The brain has no idea these are meetings. It can't route to attendees. It can't pull dates. It can't surface "this conversation came up again with the same people three weeks later."

Add a `meeting` type:

```bash
gbrain schema add-type meeting --primitive temporal --prefix meetings/ --extractable
gbrain schema sync --apply
```

The sync backfills `page.type = 'meeting'` on all 4000 pages in 1000-row batches. Now:

- `gbrain whoknows "Q3 roadmap discussion"` routes through the meeting type, ranking by `expert_routing` signal (attendees, recency, salience) instead of raw text.
- `gbrain extract-facts` runs on every meeting page automatically (because `extractable: true`), pulling typed facts like `attended_by=alice-example`, `date=2026-05-23`.
- The downstream `think` skill can now answer "what did we decide about pricing in the last three roadmap meetings" by querying the meeting graph instead of grep'ing 4000 files.

One command. 4000 pages went from invisible to queryable. The content didn't change. The structure did.

### 2. The founder ops brain

You're a founder or investor with ~500 markdown files mixing leads, portfolio companies, deal notes, intros, and follow-ups. You've been writing freely; you have no system. Your queries are all "wait, who introduced me to that fintech founder again?" and you scroll Notion for 20 minutes.

Add the founder shape:

```bash
gbrain schema fork gbrain-base mine
gbrain schema use mine

# Types
gbrain schema add-type lead       --primitive entity --prefix people/leads/         --expert
gbrain schema add-type investor   --primitive entity --prefix people/investors/     --expert --extractable
gbrain schema add-type portco     --primitive entity --prefix companies/portco/     --expert --extractable
gbrain schema add-type deal       --primitive entity --prefix companies/deals/      --extractable

# Link verbs
gbrain schema add-link-type invested-in --page-type investor --target-type portco
gbrain schema add-link-type intro-from  --page-type lead     --target-type lead
gbrain schema add-link-type passed-on   --page-type investor --target-type deal
gbrain schema add-link-type led-by      --page-type deal     --target-type investor

gbrain schema sync --apply
```

Now `gbrain whoknows "Series A SaaS"` routes through `investor` and `portco` types specifically, not the noisy general type set. `gbrain graph-query alice-example --type intro-from --depth 2` walks two hops of intros to surface "Alice introduced you to Bob who introduced you to Charlie." `gbrain extract-facts` starts producing typed claims from the fence in your deal pages: `(deals/acme-seed, raise=2000000, valuation=15000000, lead=widget-vc, closed_at=2026-05-23)`.

The CRM you've been promising yourself you'll set up next quarter? You just shipped it in 4 commands. It's downstream of your notes, not parallel to them.

### 3. The research brain

Replace "founder" with "PhD student" and the same pattern applies with different types: `researcher`, `paper`, `lab`, `grant`, `dataset` + `authored`, `cites`, `funded-by`, `uses-dataset`.

```bash
gbrain schema add-type paper --primitive annotation --prefix research/papers/ --extractable
gbrain schema add-link-type authored   --page-type researcher --target-type paper
gbrain schema add-link-type cites      --page-type paper      --target-type paper
gbrain schema add-link-type uses       --page-type paper      --target-type dataset
```

Suddenly "show me papers that cite this work AND use the same dataset" is a `gbrain graph-query` traversal, not 30 minutes in Google Scholar. The fact extraction picks up `arxiv_id=2402.04253`, `cited_by_count=140`, `published_date=2026-02-15` automatically. Your reading-list-as-markdown turns into a queryable research graph that knows who works on what and what's connected to what.

### 4. The legal brain (or any domain where claims have numbers)

Lawyers, medical providers, accountants, anyone working in a domain where the meaning of a number depends on its type. A "judgment of $5M" against a "$2M case strategy threshold" is a comparison the brain can do — but only if both numbers are typed.

```bash
gbrain schema add-type case --primitive entity --prefix legal/cases/ --extractable --expert
gbrain schema add-type motion --primitive annotation --prefix legal/motions/ --extractable
gbrain schema add-type deposition --primitive annotation --prefix legal/depositions/ --extractable
gbrain schema add-link-type filed-in --page-type motion --target-type case
gbrain schema add-link-type cites    --page-type motion --target-type precedent
```

Now `## Facts` fences in your case notes can carry typed claims (`damages=5000000`, `filed_date=2026-05-23`, `judge=jane-doe`) that gbrain stores as first-class columns. `gbrain eval trajectory legal/cases/acme-v-widget` prints the case history with regressions flagged. `gbrain founder scorecard` (renamed for legal: roll up plaintiff success rate, average damages, settlement-vs-trial ratio) gives you a structured view of how your practice is performing.

This isn't possible without typed page kinds. You can write the same prose in any note-taking app. Only gbrain treats the numbers as comparable across pages of the same type.

### 5. The team brain

`gbrain mounts add` lets you stack additional brains alongside your personal one. Each mounted brain has its OWN schema pack. The eng team's brain has `incident`, `runbook`, `service`, `oncall-rotation`. The design team's brain has `component`, `experiment`, `ab-test`, `figma-link`. The legal team's brain has cases and depositions.

When you query, the schema pack governs how each source's content is routed. An eng query against the mounted eng brain knows that `incidents/2026-05-23-db-outage.md` is an `incident` page with `severity=p0`, `mttr=47min`, `on_call=alice-example` — extractable typed facts. Your personal query against the same brain still works, but the routing is sharper because the eng team has invested in their ontology.

The schema is the team's tribal knowledge made explicit. Two engineers on different teams searching the same brain get DIFFERENT routing because their personal packs declare different expert types.

### 6. The "agent co-curates your ontology" pattern (the new thing)

This is what v0.40.7.0 actually enabled, and what the closed PR #1321 was reaching for.

Your OpenClaw (or any agent connected to your brain over HTTPS MCP with admin scope) watches your ingestion stream. After a week of you dumping notes under `garrytan/companies/yc-w24/`, the agent runs `gbrain schema detect` periodically, sees that prefix accumulating, and proposes:

> You have 47 pages under `companies/yc-w24/` typed as `company` (generic). They share a structural pattern (founder names, raise amounts, batch tag). Should I add a `yc-w24-company` type with `extractable: true` and the existing aliases pointing back to `company`? I'd backfill the 47 pages and add `cohort=W24` as a typed fact extracted from each page.

You approve once. The agent calls `schema_apply_mutations` over MCP with a batch:

```json
{
  "pack": "mine",
  "mutations": [
    {"op": "add_type", "name": "yc-w24-company", "primitive": "entity", "prefix": "companies/yc-w24/", "extractable": true, "expert_routing": true},
    {"op": "add_alias", "type": "yc-w24-company", "alias": "company"}
  ]
}
```

All inside ONE `withPackLock` scope, atomic, audited (the agent's `client_id` captured in the audit log as `actor: mcp:<clientId8>`). Cache invalidated cross-process. Sync backfills the 47 pages. The brain learned a new category of thing without you having to think about it.

The next time you query "YC W24 companies in fintech", the brain routes through the new type. Six months later when you forget the pattern entirely, the agent reminds you it's there and offers to consolidate it with the W25 batch.

The brain learns. The agent is the curator. You approve, the agent does the work.

### 7. The before-vs-after benchmark

If you want to FEEL the difference without buying the pitch:

Pick a real corpus you have. Run `gbrain whoknows` on a topic that should match. Note the top-3 results.

Then run `gbrain schema review-orphans --limit 50 --json` and look at the untyped pages. If 10+ of them share an obvious prefix that should be a real type, add the type + sync.

Re-run the same `whoknows` query. Top-3 should shift, because the new type is now routing through expert ranking instead of being lumped into the catchall. The numerical delta IS the win. You can run a tutorial in 5 minutes; this experiment proves it matters on your actual content.

## Why this matters

Three things gbrain does that generic note systems can't:

**1. The brain knows the difference between a person and an idea.** Page-type matters at query time. `gbrain whoknows` only considers `expert_routing: true` types. `gbrain extract-facts` only runs on `extractable: true` types. `gbrain graph-query` walks declared link verbs. None of that works on a flat tag system because tags don't have semantics — they're labels. Types are first-class citizens with rules attached.

**2. Untyped content is invisible content.** If your meetings are typed as `note`, expert routing skips them, facts extraction ignores them, link inference doesn't fire. They exist on disk and they're indexed for text search, but the structural surfaces (whoknows, find_experts, recall, think) treat them as second-class. Adding a type isn't cosmetic; it's structural promotion.

**3. The schema is queryable AND mutable AND auditable.** You can ask the brain what its schema looks like (`gbrain schema graph`), evolve it through 14 atomic CLI verbs + 9 MCP ops with full lock + audit semantics, and recover from any mistake (every primitive has an inverse, plus `gbrain schema downgrade` restores the previous active pack). This isn't "vibes-based knowledge management." It's a production system with structural integrity guarantees.

## What changed in v0.40.7.0 specifically

v0.39.1.0 shipped the schema-pack engine. You could ALREADY fork the bundled pack and edit `pack.yaml` by hand. What you couldn't do was let an agent author it safely — there were no atomic file locks, no audit log, no MCP exposure, no pack-aware wiring in the query path. The cathedral was built but unreachable from the outside.

v0.40.7.0 closed those gaps:

- **`withMutation` skeleton** wraps every primitive in 8 ordered safety steps (bundled-guard → lock → read → mutate → validate → atomic write → audit → invalidate). The pack file on disk is never partial. Two concurrent agents can't race.
- **Per-pack `O_CREAT|O_EXCL` atomic lock** (not the TOCTOU `existsSync+writeFileSync` pattern from page-lock.ts — codex caught that during plan review). TTL refresh every 10s while a mutation runs; `--force` means "steal stale lock" not "skip locking."
- **Privacy-redacted audit log** at `~/.gbrain/audit/schema-mutations-YYYY-Www.jsonl`. Type names sha8-hashed, prefixes truncated to first segment only. A leaked screenshot of the audit can't reveal sensitive taxonomy like `personal/oncology/` or `legal/depositions/`.
- **9 new MCP ops** including the batched `schema_apply_mutations` (admin scope, NOT localOnly — your OpenClaw and any remote agent author packs over normal HTTPS MCP, with `client_id` captured as `actor: mcp:<clientId8>`).
- **T1.5 wiring** finally completes for `whoknows` and `find_experts`: a custom `researcher` type marked `--expert` now actually surfaces in query results. Pre-v0.40.7 it silently never matched because the query path read hardcoded `['person', 'company']`.
- **Cross-process invalidation** via stat-mtime TTL gate inside `loadActivePack`. Operator runs `gbrain schema add-type` from a terminal; the autopilot daemon picks up the new type within 1 second without a restart.

The cumulative effect: an agent can safely co-curate your ontology with a complete forensic trail. That's the new thing.

## Where to start

- **Want to see it work in 5 minutes?** Run the [tutorial](schema-author-tutorial.md). Forks the bundled pack, adds a researcher type, proves the wiring end-to-end.
- **Want the agent recipe?** Read [`skills/schema-author/SKILL.md`](../skills/schema-author/SKILL.md). 7-phase workflow agents follow when they detect a schema-evolution opportunity.
- **Want the rules of thumb?** Read [`skills/conventions/schema-evolution.md`](../skills/conventions/schema-evolution.md). Decision tree for when to add a type vs alias vs prefix. <20 pages don't pack-codify. 100+ pages need first-class types.
- **Want the architecture?** The "Schema Cathedral v3 (v0.40.7.0)" section in `CLAUDE.md` has the 14-bullet module-by-module breakdown, each citing the design decision and codex finding that motivated it.
- **Want to set up an agent that co-curates your brain?** Run `gbrain auth register-client my-agent --scopes admin` to mint an OAuth client your remote agent can use to call `schema_apply_mutations` over MCP. The agent then runs detect → suggest → apply on its own cadence and asks you to approve substantive changes.

The killer feature isn't "schemas." Personal knowledge systems have had schemas forever. The killer feature is that your AGENT can shape them safely on your behalf, with structural integrity guarantees that match what you'd expect from a database, not a notes app.

That's what we built. Try it on a corpus you actually have and the numbers go up.

---

## docs/schema-author-tutorial.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/schema-author-tutorial.md

# Tutorial: Build your first schema pack

You'll fork the bundled `gbrain-base` pack, add a custom `researcher` page type, import a handful of placeholder researcher pages, backfill their `page.type` column with one command, then prove the wiring works by running `gbrain whoknows` and seeing your new type surface in results. End state: a forked-and-active pack on disk, ~5 pages typed as `researcher`, and a query that proves the pack-aware routing fires end-to-end.

**Want the WHY before the HOW?** Read [`what-schemas-unlock.md`](what-schemas-unlock.md) first — 7 concrete use cases (4000 invisible meetings, the founder ops brain, the research brain, the legal brain, the team brain, agent-as-co-curator) plus the structural argument for why types matter at query time. Then come back here for the 5-minute walkthrough.

The whole walkthrough takes about 5 minutes. You'll see something working by step 3.

## What you'll need

- gbrain v0.40.7.0 or later (`gbrain --version` to check)
- A brain that's been initialized (`gbrain init` already run; either PGLite or Postgres is fine)
- A terminal you can paste commands into

That's it. No API keys required for this tutorial — every step works against the bundled pack and local-only commands.

## Step 1: See what pack is active today

```bash
gbrain schema active --json
```

You'll see something like:

```json
{
  "pack_name": "gbrain-base",
  "version": "1.0.0",
  "sha8": "...",
  "page_types_count": 22,
  "source_tier": "default"
}
```

`source_tier: "default"` means you haven't customized anything — you're on the bundled pack. `page_types_count: 22` is the universal starter (person, company, meeting, note, etc.).

**You can't mutate bundled packs directly.** Step 2 forks it so you have something writable.

## Step 2: Fork the bundled pack

```bash
gbrain schema fork gbrain-base mine
```

Output: `Forked 'gbrain-base' → 'mine' at ~/.gbrain/schema-packs/mine/pack.json`.

The fork is a byte-for-byte copy of `gbrain-base` living at `~/.gbrain/schema-packs/mine/pack.json`. Now you have a writable pack you can mutate.

## Step 3: Activate the fork

```bash
gbrain schema use mine
```

Output: `Pack: mine (json) ... Active.`

Run `gbrain schema active --json` again to confirm `pack_name` is now `mine` and `source_tier` is `home-config` (read from `~/.gbrain/config.json`).

**You've already accomplished something visible** — the active pack changed, and any future query will route through your fork. The next four steps add a custom type and prove it works.

## Step 4: Add a researcher type

```bash
gbrain schema add-type researcher \
  --primitive entity \
  --prefix people/researchers/ \
  --extractable \
  --expert
```

Output: `Pack: mine (json)` + `Sha8: <prev> → <new>`.

What just happened:
- The mutation went through `withMutation`'s 8-step skeleton: bundled-guard → per-pack lock → read → mutate → file-plane lint validation → atomic write → audit log → cache invalidation.
- The pack now declares `researcher` as an entity primitive bound to `people/researchers/`, marked `extractable: true` (eligible for facts extraction) and `expert_routing: true` (surfaces in `whoknows` queries).
- An audit row landed in `~/.gbrain/audit/schema-mutations-YYYY-Www.jsonl` with your type name SHA-8-redacted and the prefix's first segment only (`people`) for privacy.

Verify the type is in the pack:

```bash
gbrain schema explain researcher
```

You'll see the resolved settings printed back.

## Step 5: Import some placeholder researcher pages

You need pages under `people/researchers/` for the next step to do anything. If your brain repo already has them, skip ahead. If not, drop 3-5 placeholder markdown files into `<your-brain-repo>/people/researchers/` and import:

```bash
mkdir -p people/researchers
cat > people/researchers/alice-example.md <<'EOF'
---
title: Alice Example
---

ML researcher at Example Lab. Works on contrastive embeddings.
EOF

cat > people/researchers/bob-example.md <<'EOF'
---
title: Bob Example
---

Vision researcher at Widget University. Recent paper on diffusion models.
EOF

cat > people/researchers/charlie-example.md <<'EOF'
---
title: Charlie Example
---

RL researcher at Acme Research. Focus on inverse reinforcement learning.
EOF

gbrain sync
```

The sync imports the new files. They'll be stored in the database but their `type` column will still be empty — the new type was added to the pack AFTER these pages already existed (the typical real-world scenario for an agent walking into an existing brain).

## Step 6: See the gap with `stats`

```bash
gbrain schema stats --json | jq '.aggregate, .dead_prefixes'
```

You'll see `untyped_pages: 3` (or however many you just imported) and `dead_prefixes: []` — your new prefix has 3 matching pages, so it's not dead.

The 3 researcher pages are "orphaned" by type even though they live in the right directory. The next step backfills them.

## Step 7: Backfill with `sync --apply`

First dry-run to see what would happen:

```bash
gbrain schema sync --json
```

You'll see something like:

```json
{
  "schema_version": 1,
  "apply": false,
  "per_prefix": [
    {
      "type": "researcher",
      "prefix": "people/researchers/",
      "would_apply": 3,
      "sample_slugs": ["people/researchers/alice-example", "people/researchers/bob-example", "people/researchers/charlie-example"],
      "applied": 0
    }
  ],
  "total_would_apply": 3,
  "total_applied": 0
}
```

`would_apply: 3` is what you'd touch. `sample_slugs` is the agent's drilldown signal — if those slugs look wrong, abort. They look right, so apply:

```bash
gbrain schema sync --apply
```

You'll see per-batch progress lines on stderr and a final `total_applied: 3`. The UPDATE ran in chunks of 1000 (yours fit in one chunk) and never wedged any concurrent writer.

## Step 8: Prove the wiring works

```bash
gbrain whoknows "machine learning"
```

If your researcher pages contain ML-related content, they'll surface in the ranked results — even though they're typed `researcher`, not `person` or `company`.

**This is the load-bearing demonstration of T1.5 wiring.** Pre-v0.40.7.0, `whoknows` hardcoded `['person', 'company']` as the eligible types and would have ignored your `researcher` pages entirely. The v0.40.7.0 wiring consults the active pack's `expert_routing: true` types via `expertTypesFromPack(pack.manifest)`, so your custom type now routes through expert search.

## What you built

You now have:
- A fork of `gbrain-base` named `mine` at `~/.gbrain/schema-packs/mine/pack.json`, active in your brain via `~/.gbrain/config.json`.
- A `researcher` page type registered in the pack with `entity` primitive, `people/researchers/` prefix, `extractable: true`, `expert_routing: true`.
- 3 pages typed as `researcher` (backfilled from disk via `gbrain schema sync --apply`).
- A query path that routes through the new type: `gbrain whoknows` reads the pack and includes `researcher` in its type filter.

You also exercised the full mutation skeleton: bundled-pack guard, per-pack lock, validation gate, atomic write, audit log, cache invalidation. Every step was idempotent — re-running any of them is a no-op.

## Next steps

**Add a link verb.** A `researcher` can `author` a `paper`. To model that:

```bash
gbrain schema add-type paper --primitive annotation --prefix research/papers/ --extractable
gbrain schema add-link-type authored --page-type researcher --target-type paper
gbrain schema graph
```

The graph now shows `researcher --(authored)--> paper`.

**Add aliases for query closure.** If you want `gbrain query researcher` to also surface `person` rows (because researchers ARE people):

```bash
gbrain schema add-alias researcher person
```

Read [`skills/conventions/schema-evolution.md`](../skills/conventions/schema-evolution.md) for the decision tree on when to add types vs aliases vs prefixes. The short version: <20 pages → don't pack-codify; 20-100 → alias on existing type; 100+ → first-class type.

**Lint your pack before shipping.** The 11-rule lint surface (with the optional `--with-db` flag for DB-aware checks) catches dangling references, prefix collisions, and dead-corpus warnings:

```bash
gbrain schema lint --with-db
```

**Commit your pack to source control.** If `~/.gbrain/schema-packs/mine/` is a git repo, commit `pack.json` and push. Your pack survives across machines, and the `mutation_count_anomaly` lint rule will nudge you when you hit >50 mutations in a week (the "you should be committing this" signal).

**For agents (MCP):** the same operations are reachable over HTTPS MCP via 9 new ops. Register an admin-scope OAuth client and `schema_apply_mutations` lets a remote agent compose multi-step refactors as one atomic batch. The batched MCP op + per-pack lock + audit log are the load-bearing primitives that make remote schema authoring safe. See [`skills/schema-author/SKILL.md`](../skills/schema-author/SKILL.md) for the agent dispatcher.

**Undo a mistake.** Every mutation primitive has an inverse (`remove-type`, `remove-alias`, `remove-prefix`, `remove-link-type`, `set-extractable false`, etc.). If you fork twice and want to revert, `gbrain schema downgrade` restores the previous active pack from `~/.gbrain/schema-pack-history.jsonl`.

## Related docs

- **Reference:** `gbrain schema --help` for the full 22-verb CLI surface; CLAUDE.md's "Schema Cathedral v3 (v0.40.7.0)" section for the module-by-module architecture.
- **How-to:** [`skills/schema-author/SKILL.md`](../skills/schema-author/SKILL.md) — the agent dispatcher with the 7-phase workflow (brain → assess → propose → apply → sync → verify → commit).
- **Explanation:** [`skills/conventions/schema-evolution.md`](../skills/conventions/schema-evolution.md) — when to add a type vs alias vs prefix.
- **Plan + decisions:** the original design captured 21 decisions including the bundled-pack guard rationale (D6), the empty-filter fallback contract (D4), and the MCP non-localOnly trust posture (D2). Lives in `~/.claude/plans/system-instruction-you-are-working-recursive-thacker.md` (private).

---

## docs/guides/live-sync.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/guides/live-sync.md

# Live Sync: Keep the Index Current

## Goal

Every markdown change in the brain repo is searchable within minutes, automatically, with no manual intervention.

## What the User Gets

Without this: you correct a hallucination in a brain page, but the vector DB
keeps serving the old text because nobody ran `gbrain sync`. Stale search
results erode trust. The brain becomes unreliable.

With this: edits show up in search within minutes. The vector DB stays current
with the brain repo automatically. You never have to remember to run sync.

## Implementation

### Prerequisite: Session Mode Pooler

Sync uses `engine.transaction()` on every import. If `DATABASE_URL` points to
Supabase's **Transaction mode** pooler, sync will throw `.begin() is not a
function` and **silently skip most pages**. This is the number one cause of
"sync ran but nothing happened."

Fix: use the **Session mode** pooler string (port 6543, Session mode) or the
direct connection (port 5432, IPv6-only). Verify by running `gbrain sync` and
checking that the page count in `gbrain stats` matches the syncable file count
in the repo.

### The Primitives

Always chain sync + embed:

```bash
gbrain sync --repo /path/to/brain && gbrain embed --stale
```

- `gbrain sync --repo <path>` -- one-shot incremental sync. Detects changes via
  `git diff`, imports only what changed. For small changesets (<= 100 files),
  embeddings are generated inline during import.
- `gbrain embed --stale` -- backfill embeddings for any chunks that don't have
  them. Safety net for large syncs (>100 files) or prior `--no-embed` runs.
- `gbrain sync --watch --repo <path>` -- foreground polling loop, every 60s
  (configurable with `--interval N`). Embeds inline for small changesets. Exits
  after 5 consecutive failures, so run under a process manager or pair with a
  cron fallback.

### Approach 1: Cron Job (recommended)

Run every 5-30 minutes. Works with any cron scheduler.

```bash
gbrain sync --repo /data/brain && gbrain embed --stale
```

**OpenClaw:**
```
Name: gbrain-auto-sync
Schedule: */15 * * * *
Prompt: "Run: gbrain sync --repo /data/brain && gbrain embed --stale
  Log the result. If sync fails with .begin() is not a function,
  the DATABASE_URL is using Transaction mode pooler."
```

**Hermes:**
```
/cron add "*/15 * * * *" "Run gbrain sync --repo /data/brain &&
  gbrain embed --stale. Log the result." --name "gbrain-auto-sync"
```

### Approach 2: Long-Lived Watcher

For near-instant sync (60s polling). Run under a process manager that
auto-restarts on exit. Pair with a cron fallback since `--watch` exits
on repeated failures.

```bash
gbrain sync --watch --repo /data/brain
```

### Approach 3: Git Hook / Webhook

Triggers sync on push events for instant sync (<5s).

- **GitHub webhook:** Set up the webhook to call
  `gbrain sync --repo /data/brain && gbrain embed --stale`.
  Verify `X-Hub-Signature-256` against a shared secret.
- **Git post-receive hook:** If the brain repo is on the same machine.

### What Gets Synced

Sync only indexes "syncable" markdown files. These are excluded by design:
- Hidden paths (`.git/`, `.raw/`, etc.)
- The `ops/` directory
- Meta files: `README.md`, `index.md`, `schema.md`, `log.md`

### Sync is Idempotent

Concurrent runs are safe. Two syncs on the same commit no-op because content
hashes match. If both a cron and `--watch` fire simultaneously, no conflict.

## Tricky Spots

1. **Always chain sync + embed.** Running `gbrain sync` without
   `gbrain embed --stale` leaves new chunks without embeddings. They exist
   in the database but are invisible to vector search. Always run both
   commands together. The `&&` ensures embed only runs if sync succeeds.

2. **--watch polls, it doesn't stream.** The `--watch` flag polls every 60s
   (configurable). It is not a filesystem watcher or git hook. It exits after
   5 consecutive failures, so it needs a process manager (systemd, pm2) or a
   cron fallback to stay alive. Don't assume it runs forever.

3. **Webhook needs the server running.** If you use a GitHub webhook for
   instant sync, the receiving server must be running and reachable. If the
   server is down when a push happens, that sync is missed. Pair webhooks
   with a cron fallback that catches anything the webhook missed.

## How to Verify

1. **Edit a file and search for the change.** Edit a brain markdown file,
   commit, and push. Wait for the next sync cycle (cron interval or `--watch`
   poll). Run `gbrain search "<text from the edit>"`. The updated content
   should appear in results. If it returns old content, sync failed.

2. **Compare page count to file count.** Run `gbrain stats` and count the
   syncable markdown files in the brain repo. The page count in the database
   should match. If they diverge, files are being silently skipped (likely
   a Transaction mode pooler issue).

3. **Check embedded chunk count.** In `gbrain stats`, the embedded chunk
   count should be close to the total chunk count. A large gap means
   `gbrain embed --stale` isn't running after sync, leaving chunks invisible
   to vector search.

---

*Part of the [GBrain Skillpack](../GBRAIN_SKILLPACK.md).*

---

## docs/guides/cron-schedule.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/guides/cron-schedule.md

# Reference Cron Schedule

## Goal

A production brain runs 20+ recurring jobs that keep it alive, current, and
compounding. This guide shows the schedule, the patterns, and how to set it up.

## What the User Gets

Without this: the brain only updates when you manually ingest data. Pages go
stale, entities are thin, citations break, and the agent answers from old context.

With this: the brain maintains itself. Email, social, calendar, and meetings
flow in automatically. Thin pages get enriched overnight. Broken citations get
fixed. You wake up and the brain is smarter than when you went to sleep.

## The Schedule

| Frequency | Job | Brain Interaction | Recipe |
|-----------|-----|-------------------|--------|
| Every 30 min | Email monitoring | Search sender, update people pages | [email-to-brain](../../recipes/email-to-brain.md) |
| Every 30 min | X/Twitter collection | Create/update media pages, entity extraction | [x-to-brain](../../recipes/x-to-brain.md) |
| 3x/day (weekdays) | Meeting sync | Full ingestion + attendee propagation | [meeting-sync](../../recipes/meeting-sync.md) |
| Weekly | Calendar sync | Daily files + attendee enrichment | [calendar-to-brain](../../recipes/calendar-to-brain.md) |
| Daily AM | Morning briefing | Search calendar attendees, deal status, active threads | [briefing skill](../../skills/briefing/SKILL.md) |
| Weekly | Brain maintenance | `gbrain doctor`, embed stale, orphan detection | [maintain skill](../../skills/maintain/SKILL.md) |
| Nightly | Dream cycle | Entity sweep, enrich thin spots, fix citations | See below |

## Implementation: Setting Up Cron Jobs

```bash
# Email collector — every 30 minutes
*/30 * * * * cd /path/to/email-collector && node email-collector.mjs collect && node email-collector.mjs digest

# X/Twitter collector — every 30 minutes
*/30 * * * * cd /path/to/x-collector && node x-collector.mjs collect >> /tmp/x-collector.log 2>&1

# Meeting sync — 10 AM, 4 PM, 9 PM on weekdays
0 10,16,21 * * 1-5 cd /path/to/meeting-sync && node meeting-sync.mjs >> /tmp/meeting-sync.log 2>&1

# Calendar sync — Sundays at 10 AM
0 10 * * 0 cd /path/to/calendar-sync && node calendar-sync.mjs --start $(date -v-7d +%Y-%m-%d) --end $(date +%Y-%m-%d)

# Brain health — weekly Mondays at 6 AM
0 6 * * 1 gbrain doctor --json >> /tmp/gbrain-health.log 2>&1 && gbrain embed --stale

# Dream cycle — nightly at 2 AM
0 2 * * * /path/to/dream-cycle.sh
```

### Quiet Hours Gate (MANDATORY)

Every cron job that sends notifications MUST check quiet hours first.
See [Quiet Hours](quiet-hours.md) for the full pattern.

```bash
# In every cron script:
if ! bash scripts/quiet-hours-gate.sh; then
  mkdir -p /tmp/cron-held
  echo "$OUTPUT" > /tmp/cron-held/$(basename "$0" .sh).md
  exit 0
fi
# Not quiet hours — send normally
```

### Travel-Aware Timezone Handling

The agent reads your calendar for flights, hotels, and out-of-office blocks to
infer your current location and timezone. All times shown in YOUR local timezone.

```
// Example: user flew to Tokyo
// 2 PM Pacific = 3 AM Tokyo = quiet hours
// Hold the notification, fold into morning briefing

get_user_timezone():
  calendar = gbrain search "flight" --type calendar --recent 7d
  if recent_flight:
    return infer_timezone(flight.destination)
  return config.default_timezone  // fallback: US/Pacific
```

When you travel: cron jobs that would fire during your waking hours at home but
hit your sleeping hours at the destination get held and folded into the next
morning briefing. Zero config change needed.

## The Dream Cycle

The most important cron job. Runs while you sleep.

### What It Does

```
dream_cycle():
  // Phase 1: Entity Sweep
  conversations = get_todays_conversations()
  for message in conversations:
    entities = detect_entities(message)
    for entity in entities:
      page = gbrain search "{entity.name}"
      if not page:
        create_page(entity)        // new entity, create + enrich
      elif page.is_thin():
        enrich_page(entity)        // thin page, fill it out
      else:
        update_timeline(entity)    // existing page, add today's mentions

  // Phase 2: Fix Broken Citations
  pages = gbrain list --type person --limit 100
  for page in pages:
    for entry in page.timeline:
      if not entry.has_source_attribution():
        fix_citation(entry)        // add [Source: ...] where missing
      if entry.has_tweet_url() and not entry.url_is_valid():
        fix_url(entry)             // broken tweet links

  // Phase 3: Consolidate Memory
  patterns = detect_patterns_across_conversations()
  for pattern in patterns:
    promote_to_memory(pattern)     // ephemeral → durable knowledge

  // Phase 4: Sync
  gbrain sync --no-pull --no-embed
  gbrain embed --stale
```

### Setting Up the Dream Cycle

**OpenClaw:** Ships with DREAMS.md as a default skill. Three phases (light,
deep, REM) run automatically during quiet hours.

**Hermes Agent:**
```bash
/cron add "0 2 * * *" "Dream cycle: search today's sessions for
  entities I mentioned. For each person, company, or idea: check
  if a brain page exists (gbrain search), create or update it if
  thin. Fix any broken citations. Then consolidate: read MEMORY.md,
  promote important signals, remove stale entries."
  --name "nightly-dream-cycle"
```

**Claude Code / Custom agents:** Create a script:
```bash
#!/bin/bash
# dream-cycle.sh

# Check quiet hours (should be quiet — that's when we run)
echo "Dream cycle starting at $(date)"

# Phase 1: Entity sweep (spawn sub-agent)
# Read today's conversation logs, extract entities, update brain

# Phase 2: Citation hygiene
gbrain doctor --json | jq '.checks[] | select(.status=="warn")'

# Phase 3: Embed any stale content
gbrain embed --stale

echo "Dream cycle complete at $(date)"
```

## Tricky Spots

1. **The dream cycle is NOT optional.** Without it, signal leaks out of every
   conversation. With it, nothing is lost. This is the difference between an
   agent that forgets and one that remembers.

2. **Quiet hours gate on EVERY notification job.** If you skip it, the user
   gets pinged at 3 AM. One 3 AM ping and they'll disable the whole system.

3. **Don't over-cron.** 20+ jobs sounds like a lot. Start with: email (30 min),
   dream cycle (nightly), brain health (weekly). Add more as you add
   integration recipes.

4. **Timezone changes are automatic.** Don't make the user reconfigure cron
   when they travel. Read the calendar, infer the timezone, adjust delivery.

5. **Held messages MUST be picked up.** If quiet hours hold a notification,
   the morning briefing MUST include it. Otherwise information is lost.

## How to Verify

1. **Quiet hours:** Set quiet hours to current hour. Run a notification cron.
   Verify output went to `/tmp/cron-held/`, not to messaging.
2. **Dream cycle:** Run the dream cycle manually. Check that thin entity pages
   got enriched and broken citations were fixed.
3. **Email collector cron:** Wait 30 minutes. Check `data/digests/` for new digest.
4. **Morning briefing:** Check that held messages appear in the briefing.
5. **Health check:** Run `gbrain doctor --json`. All checks should pass.

---

*Part of the [GBrain Skillpack](../GBRAIN_SKILLPACK.md). See also: [Quiet Hours](quiet-hours.md), [Operational Disciplines](operational-disciplines.md)*

---

## docs/guides/quiet-hours.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/guides/quiet-hours.md

# Quiet Hours and Timezone-Aware Delivery

## Goal

Hold all notifications during sleep hours, merge held messages into the morning briefing, and adjust automatically when the user travels.

## What the User Gets

Without this: 3 AM pings from cron jobs. One bad notification and the user
disables the entire system.

With this: the brain works overnight (dream cycle, collectors, enrichment)
but notifications are held until morning. Travel to Tokyo? The system adjusts
automatically from your calendar, no config change needed.

## Implementation

### Quiet Hours Gate

Every cron job that sends notifications must check quiet hours FIRST.

```
QUIET_START = 23  // 11 PM local time
QUIET_END = 8     // 8 AM local time

is_quiet(local_hour):
  return local_hour >= QUIET_START OR local_hour < QUIET_END
```

**Before sending any notification:**
1. Determine user's current timezone (from config or heartbeat state)
2. Convert current UTC time to local time
3. If quiet hours: hold the message, don't send

### Held Messages

During quiet hours, output goes to a held directory instead of being sent:

```
if is_quiet():
  mkdir -p /tmp/cron-held/
  write("/tmp/cron-held/{job-name}.md", output)
  exit  // don't send
else:
  send(output)
```

The morning briefing picks up held messages:

```
morning_briefing():
  held_files = list("/tmp/cron-held/*.md")
  if held_files:
    briefing += "## Overnight Updates\n\n"
    for file in held_files:
      briefing += read(file)
      delete(file)
```

This way nothing is lost. Overnight cron results get folded into the
first thing the user sees in the morning.

### Timezone Awareness

The agent should know what timezone the user is in. Store it in
the agent's operational state:

```json
{
  "currentLocation": {
    "timezone": "US/Pacific",
    "city": "San Francisco"
  }
}
```

**Update the timezone when:**
- Calendar shows the user flying somewhere (check for airline/hotel events)
- User mentions being in a different city
- User's active hours shift (they're responding at 3 AM PT = they're probably traveling)

**All times shown to the user should be in their LOCAL timezone.** Never
show UTC or a timezone the user isn't in.

### Shell Implementation

```bash
#!/bin/bash
# quiet-hours-gate.sh — run before any notification

TIMEZONE="${USER_TIMEZONE:-US/Pacific}"
LOCAL_HOUR=$(TZ="$TIMEZONE" date +%H)

if [ "$LOCAL_HOUR" -ge 23 ] || [ "$LOCAL_HOUR" -lt 8 ]; then
  echo "QUIET_HOURS=true"
  exit 1  # don't send
fi

echo "QUIET_HOURS=false"
exit 0  # ok to send
```

**In cron job scripts:**
```bash
# Check quiet hours first
if ! bash scripts/quiet-hours-gate.sh; then
  mkdir -p /tmp/cron-held
  echo "$OUTPUT" > /tmp/cron-held/$(basename "$0" .sh).md
  exit 0
fi

# Not quiet hours — send normally
send_notification "$OUTPUT"
```

### Configurable Hours

Some users want different quiet hours. Store the config:

```json
{
  "quiet_hours": {
    "start": 23,
    "end": 8,
    "enabled": true
  }
}
```

Set `enabled: false` to disable quiet hours entirely (e.g., for 24/7 monitoring).

## Tricky Spots

1. **Gate on EVERY job.** The quiet hours check must run before every single
   cron job that produces notifications. If even one job skips the gate, the
   user gets a 3 AM ping and loses trust in the entire system. No exceptions.

2. **Held messages MUST be picked up.** If the morning briefing doesn't read
   `/tmp/cron-held/`, overnight results vanish silently. Verify the briefing
   skill reads and clears the held directory. Orphaned held files mean the
   pickup integration is broken.

3. **Timezone auto-detection is fragile.** Calendar-based timezone detection
   relies on the user having airline/hotel events with location data. If the
   user books travel without calendar entries, the system won't detect the
   move. Fall back to activity-hour analysis (responding at 3 AM PT = probably
   not in PT anymore) and ask the user if uncertain.

## How to Verify

1. **Set quiet hours to the current hour.** Temporarily set `QUIET_START` to
   one hour before now and `QUIET_END` to one hour after. Trigger a cron job.
   Verify the output goes to `/tmp/cron-held/` instead of being sent.

2. **Check held message pickup.** After step 1, run or simulate the morning
   briefing. Verify the held message appears in the "Overnight Updates"
   section and the file is deleted from `/tmp/cron-held/`.

3. **Verify timezone adjustment.** Change the timezone config to a zone where
   it's currently quiet hours. Trigger a notification. Verify it's held. Change
   back to your real timezone during active hours. Trigger again. Verify it sends.

---

*Part of the [GBrain Skillpack](../GBRAIN_SKILLPACK.md).*

---

## docs/guides/scaling-skills.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/guides/scaling-skills.md

# Scaling skills past 300 without drowning the context window

When an agent grows past 100 skills, a wall starts forming. Sessions take
longer to start. The model gets a little dumber about which skill to pick.
Tokens that should be powering reasoning are powering a skill catalog the
model reads on every turn whether it needs to or not.

This guide is the recipe for breaking through that wall without deleting
capabilities. Three tiers, one resolver, one safety net. Production-tested
on a 306-skill agent (Garry's OpenClaw, the agent behind Y Combinator's
president). The pattern works whether you run OpenClaw, Hermes, Claude Code,
Cursor, or your own MCP-aware agent.

## The problem

OpenClaw scans every skill file on disk at session start and injects them
into the system prompt as `<available_skills>` entries. The model sees a
name, description, and file path for each one. When a request matches, the
model reads the full SKILL.md and follows it.

This is great architecture at 50 skills. At 100, it's fine. At 200, it
starts to drag. At 300, the system prompt eats more than 25,000 tokens on
skill descriptions alone. Tokens that aren't going to reasoning, context,
or actual work.

The symptoms compound:

- Sessions take noticeably longer to start.
- The model has less room for conversation history.
- Skill routing gets fuzzier. With 300 descriptions competing for attention,
  the model occasionally picks the wrong one.
- Cost goes up because every turn carries the full skill manifest.

The naive fix is to delete skills you don't use often. Don't do this. The
whole point of skills is that capabilities compound. A gift pipeline that
fires twice a month saves 30 minutes each time it does. A flight tracker
fires once per trip and prevents a missed Uber. Deleting low-frequency
skills optimizes for prompt size at the cost of capability. You wouldn't
delete apps from your phone because the home screen is too crowded. You'd
organize them.

## The three tiers

Not all skills need to be visible to the model at all times. Some are core.
Some are specialized. Some are dormant.

### Tier A: always loaded (~35 skills)

The skills the model needs on every single turn. Brain search, email triage,
calendar, meeting ingestion, content creation, the executive assistant.
They stay in the system prompt's `<available_skills>` manifest. The model
sees them natively and routes to them without any lookup.

### Tier B: resolver-routed (~85 skills)

Real, active skills that fire regularly but don't need to pollute every
turn. Gift pipeline, flight tracker, investor update ingestion, adversary
tracking, book mirror, civic intelligence. They live on disk. They have
full SKILL.md files. But OpenClaw doesn't inject them into the prompt.

Instead, a compact RESOLVER.md handles routing. One line per skill with
trigger phrases:

```markdown
- **gift-advisor**: gift idea | what should I bring | birthday gift | housewarming
- **flight-tracker**: track my flight | flight status | when does my flight land
- **investor-update-ingest**: investor update | portfolio update | company metrics
```

When the model sees "what should I bring to Jessica's dinner," it checks
the resolver, finds `gift-advisor`, reads the SKILL.md, and executes. Same
result. Zero wasted tokens on the other 84 turns where gifts aren't relevant.

### Tier C: dormant (~180 skills)

Built-in OpenClaw skills that aren't in active rotation (1Password, Discord,
Notion, Trello, integrations you haven't wired up yet) plus specialized
skills that almost never fire. They're explicitly disabled in the config
with `enabled: false`. They exist on disk as documentation and potential.
Flip one boolean to wake them up. Zero tokens contributed to every prompt
until then.

### The numbers

Before tiering, on Garry's 306-skill OpenClaw:

| Metric | Before |
|---|---|
| Skills in system prompt | 306 |
| Skill-description tokens per turn | ~25,000 |
| Skill routing accuracy | degrading |
| Session startup | slow |

After tiering:

| Metric | After |
|---|---|
| Skills in system prompt (Tier A) | 35 |
| Skill-description tokens per turn | ~4,000 |
| Skills still accessible (A + B + C) | 301 |
| Capability loss | zero |
| **Tokens freed per turn** | **~21,000** |

21K tokens per turn is not a small optimization. It's the difference between
the model having room to think and the model being squeezed. It's the
difference between carrying 3 pages of conversation history and carrying 15.

## What the resolver actually does

The resolver is cheaper than the manifest. That's the load-bearing insight.

OpenClaw's native skill manifest puts ~80 tokens per skill into the system
prompt (name + description + location). At 300 skills that's 24,000 tokens
spent every turn whether the model needs the catalog or not.

The resolver puts ~15 tokens per skill into a compact markdown list. At
300 skills that's 4,500 tokens. But it only fires when the model checks
it, which is only when the request doesn't match a Tier A skill. Most
turns, the resolver costs zero tokens because the Tier A match handles it.

This is the routing-table pattern but applied to the skill manifest itself.
The resolver routes to skills, but it also routes around skills, keeping
them out of the context window until they're needed.

GBrain ships with a [bundled `skills/RESOLVER.md`](../../skills/RESOLVER.md)
you can use as a reference shape. The skillpack story for distributing
your own resolvers across machines is covered in
[skillpacks as scaffolding](skillpacks-as-scaffolding.md).

## The compact list format (v0.41.7.0)

GBrain's resolver parser used to require markdown tables:

```markdown
| Trigger | Skill |
|---------|-------|
| "gift idea" | `skills/gift-advisor/SKILL.md` |
```

That's fine when you have 20 entries. It gets unwieldy at 200, and at 300
it's unreadable. OpenClaw deployments quietly evolved a compact list
format that scales better:

```markdown
- **gift-advisor**: gift idea | what should I bring | birthday gift
- **flight-tracker**: track my flight | flight status | when does my flight land
```

Before v0.41.7.0, `gbrain doctor` only spoke the table dialect. On a
306-skill compact-format resolver, the doctor reported every skill as
unreachable: **238 FAIL errors on every doctor run**. The parser was
silently treating the compact dialect as zero skills.

v0.41.7.0 ships dual-format support. The same `parseResolverEntries`
function reads both table rows and list rows in the same file, with the
v0.31.7 multi-resolver merge (skillpack `skills/RESOLVER.md` + workspace
`../AGENTS.md`) folding everything into one unified view. Run `gbrain doctor`
and the 238 FAILs collapse to 0.

### The list-format contract

A few rules to keep the parser unambiguous:

- **Skill names must be kebab-lowercase.** `gift-advisor`, `flight-tracker`,
  `email-triage`. Names that start with an uppercase letter (`MyTool`,
  `Note`, `Convention`) are deliberately ignored. This is what stops prose
  bullets like `- **Note**: see [link]` from being mis-parsed as skill
  rows in real-world AGENTS.md files.
- **The path always resolves to `skills/<name>/SKILL.md`.** An optional
  `→ \`skills/path\`` (or ASCII `->`) suffix is allowed for readability,
  but the parser strips it. For non-conventional paths (skills under
  nested directories, references into `conventions/`, anything that
  isn't `skills/<name>/SKILL.md`), use the table format.
- **Triggers separate with `|`.** Empty pieces and the literal `...`
  placeholder are dropped. Each trigger becomes its own resolver entry,
  all pointing at the same skill.
- **Bold or plain.** `- **name**: triggers` is preferred. `- name: triggers`
  works as a fallback.

You can mix table and list rows in the same file. Useful when a brain
inherits a table-format `RESOLVER.md` from gbrain and a list-format
`../AGENTS.md` from OpenClaw.

## The doctor safety net

The danger with tiering is invisible skill loss. You disable a skill from
native scanning, forget to add it to the resolver, and now the agent can't
do something it used to do. You won't notice until the moment you need it.

`gbrain doctor` walks every skill on disk and verifies it's reachable,
either through native scanning (Tier A) or through the resolver (Tier B
and C). On Garry's setup, the first run after tiering found 63 unreachable
skills. Sixty-three capabilities that existed on disk but had no routing
path. Fixed in an hour by adding resolver entries.

Run it after every skill change:

```bash
gbrain doctor
```

For CI gates, use the JSON-emitting variant:

```bash
gbrain check-resolvable --json
gbrain check-resolvable --strict  # warnings fail too
```

If a skill is unreachable, the output tells you which one and suggests
the fix. The resolver is a document. Documents are cheap to fix.

## Implementation walkthrough

Three changes. Total time about 45 minutes once you've decided which
skills go in which tier.

### 1. Audit and tier your skills

Walk through every skill. Ask: does this need to fire on every turn?

- If yes → Tier A.
- If it fires weekly or less but is real → Tier B.
- If you don't use it → Tier C.

### 2. Disable Tier B and C in your agent's config

For OpenClaw, the file is `openclaw.json`. Add an entry per disabled skill:

```json
{
  "skills": {
    "entries": {
      "gift-advisor": { "enabled": false },
      "flight-tracker": { "enabled": false },
      "1password": { "enabled": false }
    }
  }
}
```

The exact config shape depends on which agent runtime you use. The point
is the same in all of them: tell the runtime not to inject this skill into
the system prompt. The file stays on disk; only the prompt injection stops.

### 3. Write the resolver

One line per Tier B and Tier C skill. Trigger phrases that match how you
actually ask for things:

```markdown
- **gift-advisor**: gift idea | what should I bring | birthday gift
- **flight-tracker**: track my flight | flight status | when do I land
- **investor-update-ingest**: investor update | portfolio update | company metrics
```

That's it. The model handles the rest. When a request doesn't match Tier A,
it checks the resolver, reads the matching SKILL.md, and executes.

### 4. Run `gbrain doctor` and fix any unreachable skills

The doctor sweep tells you which skills don't have a routing path. Add a
resolver entry for each one, re-run, repeat until the count is zero.

## A lesson from the first version

I initially converted my resolver from a clean list format to a table
format because the validator only spoke tables. That was wrong. When a
tool fails against valid data, the right move is to fix the tool, not
reshape the data. The list format was correct, compact, readable, easy
to maintain. The parser needed to support both shapes. v0.41.7.0 is
that fix.

The same principle applies everywhere in agent systems. Your SKILL.md is
the source of truth. Your AGENTS.md is the source of truth. Your resolver
is the source of truth. When tooling disagrees with your configuration,
the tooling is wrong. Fix the tooling.

## The scaling curve

At 50 skills, you don't need any of this. Just load everything.

At 100, you start feeling the drag but can push through.

At 200, routing accuracy drops and sessions get noticeably slower. This
is where most people stop adding skills, which means their agent stops
getting more capable. Bad trade.

At 300+, tiering is mandatory. But with tiering, there's no ceiling.
1,000 skills with 35 in the hot path and 965 in the resolver is the same
per-turn cost as 35 skills with no resolver. The cost stays flat.
Capabilities compound.

The architecture that gets you from 50 to 300 is different from the
architecture that gets you from 10 to 50. That's normal. Systems that
scale change shape. The important thing is that each tier preserves full
capability. You're organizing, not deleting.

## Related

- [Skill development cycle](skill-development.md) — the 5-step loop for
  turning a repeated task into a real skill.
- [Skillpacks as scaffolding](skillpacks-as-scaffolding.md) — how to
  distribute a coherent set of skills across machines and agents.
- [Sub-agent routing](sub-agent-routing.md) — when to delegate to a
  sub-agent vs handle in-line, and the model routing table for each path.

GBrain: [github.com/garrytan/gbrain](https://github.com/garrytan/gbrain).
The `parseResolverEntries` parser lives at
[`src/core/check-resolvable.ts`](../../src/core/check-resolvable.ts);
the bundled resolver lives at [`skills/RESOLVER.md`](../../skills/RESOLVER.md).

---

## docs/mcp/DEPLOY.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/mcp/DEPLOY.md

# Deploy GBrain Remote MCP Server

> **v0.26.0+:** `gbrain serve --http` ships full OAuth 2.1 (client credentials,
> auth code + PKCE, refresh rotation, optional DCR), an embedded React admin
> dashboard at `/admin`, scoped operations, and a live SSE activity feed.
> Pre-v0.26 legacy bearer tokens still work — `verifyAccessToken` falls back
> to the `access_tokens` table and grandfathers tokens to `read+write+admin`.
> Postgres-only for the legacy fallback (the `access_tokens` table is Postgres-only);
> OAuth tables work on both PGLite and Postgres. See [SECURITY.md](../../SECURITY.md)
> for env vars and tunable defaults.

Access your brain from any device, any AI client. GBrain ships two transports:
`gbrain serve` (stdio) for local agents, and `gbrain serve --http` (v0.26.0+)
for remote clients over OAuth 2.1.

## Three Paths

### Local stdio (zero setup)

```bash
gbrain serve
```

Works with Claude Code, Cursor, Windsurf, and any MCP client that supports stdio.
No server, no tunnel, no token needed. Works on both PGLite and Postgres engines.

### Remote over OAuth 2.1 (recommended, v0.26.0+)

```bash
gbrain serve --http --port 3131
ngrok http 3131 --url your-brain.ngrok.app
gbrain serve --http --port 3131 --public-url https://your-brain.ngrok.app
```

Built-in HTTP transport with OAuth 2.1, scoped operations, an admin dashboard
at `/admin`, and a live SSE activity feed. Zero external dependencies. This is
the only path that works with ChatGPT (OAuth 2.1 + PKCE is required by the
ChatGPT MCP connector). Pass `--public-url` whenever the server is reachable
at anything other than `http://localhost:<port>` so the OAuth issuer in
discovery metadata matches what clients hit (RFC 8414 §3.3).

Supported clients:
- **ChatGPT** — requires OAuth 2.1 + PKCE. Works natively with `--http`.
- **Claude Desktop / Cowork** — OAuth 2.1 or legacy bearer tokens.
- **Perplexity** — OAuth 2.1 client credentials grant.
- **Claude Code, Cursor, Windsurf** — can use OAuth or legacy bearer.

See the [OAuth 2.1 setup](#oauth-21-setup-v100) section below.

### Remote with legacy bearer tokens (pre-v0.26 deployments) — Postgres only

```
Your AI client (Claude Desktop, Perplexity, etc.)
  → ngrok tunnel (https://YOUR-DOMAIN.ngrok.app)
  → gbrain serve --http  (built-in transport with bearer auth)
  → Postgres (pooler connection or self-hosted)
```

This requires:
1. A Postgres-backed brain (the `access_tokens` table only exists on Postgres;
   running `gbrain serve --http` against a PGLite install fails fast at startup)
2. A machine running `gbrain serve --http`
3. A public tunnel (ngrok, Tailscale, or cloud host)
4. A bearer token created via `gbrain auth create <name>`

Pre-v1.0 tokens are grandfathered as `read+write+admin` scopes when you upgrade
to the HTTP server, so no migration is required.

## OAuth 2.1 Setup (v0.26.0+)

### 1. Start the HTTP server

```bash
gbrain serve --http --port 3131
```

On first start, the server prints an **admin bootstrap token** to stderr:

```
Admin bootstrap token: 3a1f9c...
Open http://localhost:3131/admin and paste it to log in.
```

Save this token. Open `http://localhost:3131/admin` and paste it to access the
dashboard. The dashboard shows live activity, registered clients, request logs,
and per-client config export.

> **v0.26.9+:** `mcp_request_log.params` and the live SSE activity feed default
> to a redacted summary `{redacted, kind, declared_keys, unknown_key_count, approx_bytes}`.
> Declared param keys are kept (intersected against the operation's spec); unknown
> keys are counted but never named, and byte sizes round up to 1KB so size-probe
> attacks can't binary-search secret content. Operators on a personal laptop who
> want raw payloads back can pass `gbrain serve --http --log-full-params` (loud
> stderr warning fires at startup). Multi-tenant deployments should leave it on
> the redacted default.

### 2. Register OAuth clients

Register clients from the **`/admin` dashboard**:

1. Click **Register client**.
2. Enter a name (e.g. `perplexity`, `chatgpt`).
3. Pick scopes: `read`, `write`, `admin` (checkboxes).
4. Pick grant type: `client_credentials` for machine-to-machine (Perplexity,
   Claude Desktop bearer mode) or `authorization_code` for browser-based
   clients with PKCE (ChatGPT).
5. For `authorization_code` clients, paste the redirect URI.
6. Hit **Register**. The credential-reveal modal shows the `client_id` (and
   `client_secret` for confidential clients) once. Copy or Download JSON
   immediately — secrets are hashed on storage and never shown again.

Or from the CLI — faster for scripting:

```bash
gbrain auth register-client perplexity \
  --grant-types client_credentials \
  --scopes "read write"
```

**v0.34 — source-scoped clients.** Multi-source brains can scope a client's
write authority to one source and its read scope to a curated set with the
new `--source` and `--federated-read` flags:

```bash
gbrain auth register-client dept-x-agent \
  --grant-types client_credentials \
  --scopes "read write" \
  --source dept-x \
  --federated-read dept-x,shared,parent-canon
```

`--source` controls the write authority — `put_page` / `add_link` / etc only
land in `dept-x`. `--federated-read` controls the read axis independently;
queries return rows from any of the listed sources. Omit both flags for the
v0.33-compatible super-client shape. Pre-v0.34 clients are backfilled to
`source_id='default'` on `gbrain upgrade`.

Host-repo wrappers can register programmatically:

```ts
await oauthProvider.registerClientManual(
  'perplexity',
  ['client_credentials'],
  'read write',
  [],  // redirect_uris, empty for CC
);
```

For self-service client registration (Dynamic Client Registration, RFC 7591),
start the server with `--enable-dcr`. DCR is off by default.

### 3. Expose the server

**v0.34 — bind explicitly.** `gbrain serve --http` defaults to `127.0.0.1`.
To accept connections from the ngrok tunnel (or any non-loopback source),
restart with `--bind`:

```bash
gbrain serve --http --port 3131 --bind 0.0.0.0 --public-url https://your-brain.ngrok.app
```

When `--public-url` is set without `--bind`, a stderr WARN fires at
startup so the misconfiguration ("the tunnel is up but my agent gets
ECONNREFUSED") is loud.

```bash
brew install ngrok
ngrok config add-authtoken YOUR_TOKEN
ngrok http 3131 --url your-brain.ngrok.app
```

Your OAuth issuer URL becomes `https://your-brain.ngrok.app`. The MCP SDK's
router exposes the spec-compliant discovery endpoint at
`/.well-known/oauth-authorization-server`.

### 4. Scopes and localOnly

Every operation is tagged `read | write | admin`. Four operations are
`localOnly` and rejected over HTTP regardless of scope: `sync_brain`,
`file_upload`, `file_list`, `file_url`. Remote agents cannot reach local
filesystem surface area.

| Scope | What it allows |
|-------|---------------|
| `read` | `search`, `query`, `get_page`, `list_pages`, graph traversal |
| `write` | `put_page`, `delete_page`, `add_link`, `add_timeline_entry` |
| `admin` | Client management, token revocation, sweep, local-only ops |

## Legacy Bearer Token Setup

Keep using pre-v0.26 bearer tokens if you aren't ready to migrate. They
grandfather to `read+write+admin` scopes on the HTTP server.

### 1. Set up the tunnel

See the [ngrok-tunnel recipe](../../recipes/ngrok-tunnel.md) for full setup.
Quick version:

```bash
brew install ngrok
ngrok config add-authtoken YOUR_TOKEN
ngrok http 8787 --url your-brain.ngrok.app  # Hobby tier for fixed domain
```

### 2. Create access tokens

```bash
# Create a token for each client
gbrain auth create "claude-desktop"

# List all tokens
gbrain auth list

# Revoke a token
gbrain auth revoke "claude-desktop"
```

Tokens are per-client. Create one for each device/app. Revoke individually
if compromised. Tokens are stored SHA-256 hashed in your database.

### 3. Connect your AI client

- **ChatGPT:** [setup guide](CHATGPT.md) (OAuth 2.1 + PKCE, requires `gbrain serve --http`)
- **Claude Code:** [setup guide](CLAUDE_CODE.md)
- **Claude Desktop:** [setup guide](CLAUDE_DESKTOP.md) (must use GUI, not JSON config)
- **Claude Cowork:** [setup guide](CLAUDE_COWORK.md)
- **Perplexity:** [setup guide](PERPLEXITY.md)

### 4. Verify

```bash
gbrain auth test \
  https://YOUR-DOMAIN.ngrok.app/mcp \
  --token YOUR_TOKEN
```

## Operations

All 30 GBrain operations are available remotely, including `sync_brain` and
`file_upload` (no timeout limits with self-hosted server).

**Security note on `file_upload`:** remote MCP callers are confined to the working
directory where `gbrain serve` was launched. Symlinks, `..` traversal, and absolute
paths outside cwd are rejected. Page slugs and filenames are allowlist-validated
(alphanumeric + hyphens; no control chars, RTL overrides, or backslashes). Local
CLI callers (`gbrain file upload ...`) keep unrestricted filesystem access since
the user owns the machine.

## Deployment Options

See [ALTERNATIVES.md](ALTERNATIVES.md) for a comparison of ngrok, Tailscale
Funnel, and cloud hosts (Fly.io, Railway).

## Troubleshooting

**"missing_auth" error**
Include the Authorization header: `Authorization: Bearer YOUR_TOKEN`

**"invalid_token" error**
Run `gbrain auth list` to see active tokens.

**"service_unavailable" error**
Database connection failed. Check your Supabase dashboard for outages.

**Claude Desktop doesn't connect**
Remote servers must be added via Settings > Integrations, NOT
`claude_desktop_config.json`. See [CLAUDE_DESKTOP.md](CLAUDE_DESKTOP.md).

## Expected Latencies

| Operation | Typical Latency | Notes |
|-----------|----------------|-------|
| get_page | < 100ms | Single DB query |
| list_pages | < 200ms | DB query with filters |
| search (keyword) | 100-300ms | Full-text search |
| query (hybrid) | 1-3s | Embedding + vector + keyword + RRF |
| put_page | 100-500ms | Write + trigger search_vector update |
| get_stats | < 100ms | Aggregate query |

**Note:** `gbrain serve --http` shipped in v0.26.0 with OAuth 2.1 + admin
dashboard baked into the binary. The custom HTTP wrapper pattern (see
[voice recipe](../../recipes/twilio-voice-brain.md)) is still supported for
teams that need bespoke middleware, but for most remote deployments the
built-in server is the recommended path.

---

# AI providers

# Debugging

## docs/GBRAIN_VERIFY.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/GBRAIN_VERIFY.md

# GBrain Installation Verification Runbook

Run these checks after install to confirm every part of GBrain is working.
Each check includes the command, expected output, and what to do if it fails.

The most important check is #4 (live sync). "Sync ran" is not the same as
"sync worked." A sync that silently skips pages because of a pooler bug is
worse than no sync at all, because you think it's working.

---

## 1. Schema Verification

**Command:**

```bash
gbrain doctor --json
```

**Expected:** All checks return `"ok"`:
- `connection`: connected, N pages
- `pgvector`: extension installed
- `rls`: enabled on all tables
- `schema_version`: current
- `embeddings`: coverage percentage

**If it fails:** The doctor output includes specific fix instructions for each
check. See `skills/setup/SKILL.md` Error Recovery table.

---

## 2. Skillpack Loaded

**Check:** Ask the agent: "What is the brain-agent loop?"

**Expected:** The agent references GBRAIN_SKILLPACK.md Section 2 and describes
the read-write cycle: detect entities, read brain, respond with context, write
brain, sync.

**If it fails:** The agent hasn't loaded the skillpack. Run step 6 from the
install paste (read `docs/GBRAIN_SKILLPACK.md`).

---

## 3. Auto-Update Configured

**Command:**

```bash
gbrain check-update --json
```

**Expected:** Returns JSON with `current_version`, `latest_version`,
`update_available` (boolean). The cron `gbrain-update-check` is registered.

**If it fails:** Run step 7 from the install paste. See GBRAIN_SKILLPACK.md
Section 17.

---

## 4. Live Sync Actually Works

This is the most important check. Three parts.

### 4a. Coverage Check

Compare page count in the DB against syncable file count in the repo:

```bash
gbrain stats
```

Then count syncable files:

```bash
find /data/brain -name '*.md' \
  -not -path '*/.*' \
  -not -path '*/.raw/*' \
  -not -path '*/ops/*' \
  -not -name 'README.md' \
  -not -name 'index.md' \
  -not -name 'schema.md' \
  -not -name 'log.md' \
  | wc -l
```

**Expected:** Page count in `gbrain stats` should be close to the file count.
Some difference is normal (files added since last sync), but if page count is
less than half the file count, sync is silently skipping pages.

**If page count is way too low:** The #1 cause is the connection pooler bug.
Check your `DATABASE_URL`:
- If it contains `pooler.supabase.com:6543`, verify it's using **Session mode**,
  not Transaction mode.
- Transaction mode breaks `engine.transaction()` and causes `.begin() is not a
  function` errors.
- Fix: switch to Session mode pooler string, then run `gbrain sync --full`
  to reimport everything.

### 4b. Embed Check

```bash
gbrain stats
```

**Expected:** Embedded chunk count should be close to total chunk count.

**If embedded is much lower than total:**

```bash
gbrain embed --stale
```

If `OPENAI_API_KEY` is not set, embeddings can't be generated. Keyword search
still works without embeddings, but hybrid/semantic search won't.

### 4c. End-to-End Test

This is the real test. Edit a brain page, push, wait, search.

1. Edit a page in the brain repo (e.g., correct a fact on a person's page):

```bash
# Example: fix a line in Gustaf's page
cd /data/brain
# Make a small edit to any .md file
git add -A && git commit -m "test: verify live sync" && git push
```

2. Wait for the next sync cycle (cron interval or `--watch` poll).

3. Search for the corrected text:

```bash
gbrain search "<text from the correction>"
```

**Expected:** The search returns the **corrected** text, not the old version.

**If it returns old text:** Sync failed silently. Check:
- Is the sync cron registered and running?
- Is `gbrain sync --watch` still alive (if using watch mode)?
- Run `gbrain config get sync.last_run` to see when sync last ran.
- Run `gbrain sync --repo /data/brain` manually and check for errors.
- If you see `.begin() is not a function`, fix the pooler (see 4a above).

---

## 5. Embedding Coverage

**Command:**

```bash
gbrain stats
```

**Expected:** Embedded chunk count matches (or is close to) total chunk count.

**If zero or very low:** `OPENAI_API_KEY` may be missing or invalid. Check:

```bash
echo $OPENAI_API_KEY | head -c 10
```

If blank, set the key. Then:

```bash
gbrain embed --stale
```

---

## 6. Brain-First Lookup Protocol

**Check:** Ask the agent about a person or concept that exists in the brain.

**Expected:** The agent uses `gbrain search` or `gbrain query` FIRST, not grep
or external APIs. The response includes brain-sourced context with source
attribution.

**If it fails:** The brain-first lookup protocol isn't injected into the agent's
system context. See `skills/setup/SKILL.md` Phase D.

---

## 7. Knowledge Graph Wired

The v0.12.0 graph layer needs to be populated for existing brains. New writes are
auto-linked, but historical pages need a one-time backfill.

**Command:**

```bash
gbrain stats | grep -E 'links|timeline'
```

**Expected:** Both `links` and `timeline_entries` are non-zero (assuming the brain
has content with entity references and dated markdown).

**If it's zero on a brain with imported content:** Run the backfill.

```bash
gbrain extract links --source db --dry-run | head -5    # preview
gbrain extract links --source db                         # commit
gbrain extract timeline --source db
gbrain stats                                             # confirm > 0
```

**Bonus check** — graph traversal works:

```bash
# Pick any well-connected slug from your brain
gbrain graph-query people/<some-person-slug> --depth 2
```

**Expected:** Indented tree of typed edges (`--attended-->`, `--works_at-->`, etc.).
If the slug has no inbound or outbound links, try a different one or run extract
again.

**If extract finds nothing:** Your pages may not use entity-reference syntax. The
extractor matches `[Name](people/slug)`, `[Name](../people/slug.md)`, and bare
`people/slug` references. If your brain uses a different format, the auto-link
heuristics won't find them — file an issue with a sample page.

---

## 8. JSONB Frontmatter Integrity (v0.12.2)

Postgres-backed brains created before v0.12.2 had double-encoded JSONB columns
(`frontmatter->>'key'` returned NULL, GIN indexes were inert). `gbrain upgrade`
runs `gbrain repair-jsonb` automatically via the `v0_12_2` orchestrator.
Verify the repair succeeded.

**Command:**

```bash
gbrain repair-jsonb --dry-run --json
```

**Expected:** `totalRepaired: 0` across all 5 columns (`pages.frontmatter`,
`raw_data.data`, `ingest_log.pages_updated`, `files.metadata`,
`page_versions.frontmatter`). A zero count means every row is properly-typed
JSON objects, not string-encoded JSON.

**If the count is > 0:** The repair didn't run or was interrupted. Re-run
without `--dry-run`:

```bash
gbrain repair-jsonb
```

Idempotent. PGLite brains always report 0 (unaffected by the original bug).

**Bonus check** — frontmatter-keyed queries actually resolve:

```bash
gbrain call list_pages '{"frontmatterKey": "type", "frontmatterValue": "person"}'
```

If this returns rows on a brain with person pages, the JSONB path is healthy.

---

## Quick Verification (all checks in one pass)

```bash
# 1. Schema
gbrain doctor --json

# 2. Sync recency
gbrain config get sync.last_run

# 3. Page count + embed coverage
gbrain stats

# 4. Search works
gbrain search "test query from your brain content"

# 5. Catch any unembedded chunks
gbrain embed --stale

# 6. Auto-update
gbrain check-update --json

# 7. Knowledge graph populated (links + timeline > 0)
gbrain stats | grep -E 'links|timeline'

# 8. JSONB integrity (v0.12.2 — Postgres only, PGLite always 0)
gbrain repair-jsonb --dry-run --json
```

If all eight return successfully, the installation is healthy. For the full
end-to-end sync test (4c), push a real change and verify it appears in search.

---

## docs/guides/minions-fix.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/guides/minions-fix.md

# Minions fix — repairing a half-migrated install

**tl;dr:** on v0.11.1+ everything should self-heal. If Minions is partially
set up (no `~/.gbrain/preferences.json`, autopilot still inline, cron jobs
still on `agentTurn`), run:

```bash
gbrain apply-migrations --yes
```

It's idempotent. On v0.11.1 installs that already migrated it's a cheap
no-op.

## Context

v0.11.0 shipped the Minions schema, queue, worker, and migration skill —
but the migration skill itself never fired on upgrade. `runPostUpgrade`
printed the feature pitch and stopped. v0.11.0 was never released
publicly; v0.11.1 is the first public Minions ship and fixes the
mega-bug (migration fires automatically on `gbrain upgrade` and via
the `postinstall` hook).

If you're on a pre-v0.11.1 branch build (e.g. running the
`minions-jobs` branch before v0.11.1 tagged), Minions may be installed
but not wired: schema is v7, but no `~/.gbrain/preferences.json`,
autopilot still runs inline, cron jobs still call `agentTurn`.

This guide covers both paths: the canonical v0.11.1+ fix, and the
stopgap for pre-v0.11.1 binaries that don't have `apply-migrations`.

## Detecting the half-migrated state

```bash
gbrain doctor
```

If the install is half-migrated, you'll see:

```
[FAIL] minions_migration: MINIONS HALF-INSTALLED (partial migration: 0.11.0). Run: gbrain apply-migrations --yes
```

or

```
[FAIL] minions_config: MINIONS HALF-INSTALLED (schema v7+ but no ~/.gbrain/preferences.json). Run: gbrain apply-migrations --yes
```

For a machine-readable report (cron-friendly):

```bash
gbrain skillpack-check --quiet && echo healthy || echo needs_action
gbrain skillpack-check | jq -r '.actions[]'    # prints the exact commands to run
```

## The fix (v0.11.1 or later)

```bash
gbrain apply-migrations --yes
```

Reads `~/.gbrain/migrations/completed.jsonl`, diffs against the TS
migration registry, runs whatever's pending. Seven phases:

```
A. Schema        gbrain init --migrate-only
B. Smoke         gbrain jobs smoke
C. Mode          prompt (or --yes default pain_triggered)
D. Prefs         write ~/.gbrain/preferences.json
E. Host          AGENTS.md marker injection + cron rewrites for gbrain
                 builtins; JSONL TODOs for host-specific handlers
F. Install       gbrain autopilot --install (env-aware)
G. Record        append completed.jsonl status:"complete"
```

If Phase E emits TODOs for host-specific handlers (e.g. your OpenClaw's
~29 non-gbrain crons), the migration finishes with `status: "partial"`.
Your host agent walks the TODOs using `skills/migrations/v0.11.0.md` +
`docs/guides/plugin-handlers.md`, ships handler registrations in the
host repo, then re-runs `gbrain apply-migrations --yes`. Newly
registerable cron entries get rewritten and the JSONL rows mark
`status: "complete"`.

## The stopgap (pre-v0.11.1 binary, no apply-migrations yet)

If you're stuck on a branch build that doesn't have `apply-migrations`:

```bash
curl -fsSL https://raw.githubusercontent.com/garrytan/gbrain/v0.11.1/scripts/fix-v0.11.0.sh | bash
```

This bash script does what apply-migrations does from a shell environment:

1. `gbrain init --migrate-only` — schema v7.
2. `gbrain jobs smoke` — verify Minions health.
3. Prompt for `minion_mode` (defaults `pain_triggered` on non-TTY).
4. Write `~/.gbrain/preferences.json` atomically.
5. Append `~/.gbrain/migrations/completed.jsonl` with `status: "partial"`
   and `apply_migrations_pending: true`. That partial record is the
   signal to v0.11.1's `apply-migrations` to pick up remaining phases
   after the user upgrades.
6. Detect host agent repos and PRINT rewrite instructions (never
   auto-edits from a curl-piped script).
7. Print the next step: `Run: gbrain autopilot --install`.

Once v0.11.1 is installed, re-run `gbrain apply-migrations --yes` to
finish the remaining phases (host rewrites + autopilot install). The
stopgap's `status: "partial"` record is designed to resume cleanly
(it doesn't poison the permanent migration path).

## Verify the fix landed

```bash
# 1. Preferences exist and are readable
cat ~/.gbrain/preferences.json

# 2. Migration recorded
cat ~/.gbrain/migrations/completed.jsonl

# 3. Autopilot is supervising a Minions worker child
gbrain autopilot --status
ps aux | grep 'jobs work'

# 4. Jobs show up in the queue
gbrain jobs list

# 5. Any host-specific TODOs still pending
cat ~/.gbrain/migrations/pending-host-work.jsonl 2>/dev/null || echo "(none — all host work is done)"

# 6. Doctor + skillpack-check should both be clean
gbrain doctor
gbrain skillpack-check --quiet && echo ok
```

## If the fix fails

Each phase is idempotent. Re-running is safe. Common failure modes:

- **Phase B smoke fails:** the schema didn't apply. Check
  `~/.gbrain/config.json` has a valid `database_url` (or `database_path`
  for PGLite). Run `gbrain init --migrate-only` directly and look at
  the error.
- **Phase F install fails:** your host environment doesn't match any
  detected target. Pass `--target <macos|linux-systemd|ephemeral-container|linux-cron>`
  explicitly.
- **Pending host work never clears:** your host agent hasn't shipped
  handler registrations yet. Read
  `~/.gbrain/migrations/pending-host-work.jsonl`, open
  `skills/migrations/v0.11.0.md`, and follow the host-agent instruction
  manual.

## Related

- `skills/migrations/v0.11.0.md` — full migration skill for host agents.
- `skills/skillpack-check/SKILL.md` — when and how to run the health check.
- `docs/guides/plugin-handlers.md` — plugin contract for host-specific
  handlers.
- `skills/conventions/cron-via-minions.md` — the canonical cron rewrite
  pattern.

---

## docs/integrations/reliability-repair.md

Source: https://raw.githubusercontent.com/garrytan/gbrain/master/docs/integrations/reliability-repair.md

# Reliability repair (v0.12.2)

If you ran v0.12.0 on real Postgres or Supabase, two bugs may have corrupted
data already in your brain. v0.12.1 fixed the code going forward.
v0.12.2 adds detection in `gbrain doctor` and a standalone `gbrain repair-jsonb`
command for the mechanically fixable class. PGLite users are not affected.

## What got corrupted

**JSONB double-encode.** Four write sites used
`${JSON.stringify(x)}::jsonb` with postgres.js, which stored a JSONB
*string literal* instead of an object. `frontmatter ->> 'key'` returns NULL;
GIN indexes are ineffective. Affected: `pages.frontmatter`,
`raw_data.data`, `ingest_log.pages_updated`, `files.metadata`.

**Markdown body truncation.** `splitBody()` treated `---` horizontal rules
as a body/timeline delimiter, dropping everything after the first rule.
Wiki-style pages with multiple `##`/`###` sections lost the bulk of their
content at import time.

## Detect

```
gbrain doctor
```

Reports two new checks:

- `jsonb_integrity` — counts double-encoded rows per table and points you
  at `gbrain repair-jsonb`.
- `markdown_body_completeness` — heuristic for pages whose `compiled_truth`
  is suspiciously short compared to `raw_data.data ->> 'content'`.

## Repair

For JSONB (mechanically fixable):

```
gbrain repair-jsonb
```

Runs `UPDATE <table> SET <col> = (<col>#>>'{}')::jsonb WHERE jsonb_typeof(<col>) = 'string'`
across every affected column. Idempotent. Second run reports 0 rows. Use
`--dry-run` to preview, `--json` for structured output. The `v0_12_2`
migration runs this automatically on `gbrain upgrade`.

For truncated markdown bodies (source-dependent):

```
gbrain sync --force
# or per-page
gbrain import <slug> --force
```

v0.12.2 cannot recover content that was already lost if you no longer have
the source markdown file. `gbrain doctor` tells you which pages look short;
you decide whether to re-import from source or accept the truncation.

## Verify

```
gbrain doctor
```

All four `jsonb_integrity` rows should read zero. `markdown_body_completeness`
should match your expectations for the corpus.

---

# Migrations
