gbrain/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.
- `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. **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`.
- `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.
- `src/core/pglite-schema.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.
- `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`.
- `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)
- `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-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 29 languages 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.
- `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) — 36 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.
- `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) — 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.
- `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) — 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.
- `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) — 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.
- `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.
- `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) — `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`.
- `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) — `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).
- `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.
- `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.
- `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.
- `src/core/ai/gateway.ts` — unified seam for every AI call. **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/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/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/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.
- `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/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.
- `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/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`.
- `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.
- `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/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.
- `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.
- `src/core/backoff.ts` — Adaptive load-aware throttling: CPU/memory checks, exponential backoff, active hours multiplier
- `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.
- `src/commands/extract.ts` — `gbrain extract links|timeline|all [--source fs|db]`: 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()`.
- `src/commands/graph-query.ts` — `gbrain graph-query <slug> [--type T] [--depth N] [--direction in|out|both]`: typed-edge relationship traversal (renders indented tree)
- `src/core/link-extraction.ts` — 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). **v0.28.1 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. 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`).
- `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.
- `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]`: 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).
- `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/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. **v0.35.5.0:** 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`.
- `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. **v0.34.1.0 (#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.
- `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.
- `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.
- `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.
- `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.
- `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.
- `openclaw.plugin.json` — ClawHub bundle plugin manifest

### 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.

## 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/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.

## 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 v0.32.7 (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.

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/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.

**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.

## 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

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