Files
gbrain/CLAUDE.md
Garry Tan 3e21e9b69b feat: GBrain v0.6.0 — Remote MCP Server + 12 Bug Fixes (#28)
* fix: 7 bug fixes from Issue #9 and #22

- fix(mcp): use ListToolsRequestSchema/CallToolRequestSchema instead of string literals (Issue #9, PR #25)
- fix(mcp): handleToolCall reads dry_run from params instead of hardcoding false (#22 Bug #11)
- fix(search): keyword search returns best chunk per page via DISTINCT ON, not all chunks (#22 Bug #8)
- fix(search): dedup layer 1 keeps top 3 chunks per page instead of collapsing to 1 (#22 Bug #12)
- fix(engine): transaction uses scoped engine via Object.create, no shared state mutation (#22 Bug #2)
- fix(engine): upsertChunks uses UPSERT instead of DELETE+INSERT, preserves existing embeddings (#22 Bug #1)
- fix(slugs): validateSlug normalizes to lowercase, pathToSlug lowercases consistently (#22 Bug #4)
- schema: add unique index on content_chunks(page_id, chunk_index) for UPSERT support
- schema: add access_tokens and mcp_request_log tables via migration

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: embed schema.sql at build time, remove fs dependency from initSchema

initSchema() previously read schema.sql from disk at runtime via readFileSync,
which broke in compiled Bun binaries and Deno Edge Functions. Now uses a
generated schema-embedded.ts constant (run `bun run build:schema` to regenerate).

- Removes fs and path imports from postgres-engine.ts and db.ts
- Adds scripts/build-schema.sh for one-source-of-truth generation
- Adds build:schema npm script

Fixes Issue #22 Bug #6.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: 5 more bug fixes from Issue #22

- fix(file_upload): call storage.upload() in all 3 paths (operation, CLI upload, CLI sync) with rollback semantics (#22 Bug #9)
- fix(import): use atomic index counter for parallel queue instead of array.shift() race, preserve checkpoint on errors (#22 Bug #3)
- fix(s3): replace unsigned fetch with @aws-sdk/client-s3 for proper SigV4 auth, supports R2/MinIO via forcePathStyle (#22 Bug #10)
- fix(redirect): verify remote file exists before deleting local copy, skip files not found in storage (#22 Bug #5)
- deps: add @aws-sdk/client-s3

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* feat: remote MCP server via Supabase Edge Functions

Deploy GBrain as a serverless remote MCP endpoint on your existing Supabase
instance. One brain, accessible from Claude Desktop, Claude Code, Cowork,
Perplexity Computer, and any MCP client. Zero new infrastructure.

New files:
- supabase/functions/gbrain-mcp/index.ts — Edge Function with Hono + MCP SDK
- supabase/functions/gbrain-mcp/deno.json — Deno import map
- src/edge-entry.ts — curated bundle entry point (excludes fs-dependent modules)
- src/commands/auth.ts — standalone token management (create/list/revoke/test)
- scripts/deploy-remote.sh — one-script deployment
- .env.production.example — 3-value config template

Changes:
- config.ts: lazy-evaluate CONFIG_DIR (no homedir() at module scope)
- schema.sql: add access_tokens + mcp_request_log tables
- package.json: add build:edge script

Auth: bearer tokens via access_tokens table (SHA-256 hashed, per-client, revocable)
Transport: WebStandardStreamableHTTPServerTransport (stateless, Streamable HTTP)
Health: /health endpoint (unauth: 200/503, auth: postgres/pgvector/openai checks)
Excluded from remote: sync_brain, file_upload (may exceed 60s timeout)

Setup: clone, fill .env.production, run scripts/deploy-remote.sh, create token, done.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* docs: per-client MCP setup guides

- docs/mcp/DEPLOY.md — deployment walkthrough, auth, troubleshooting, latency table
- docs/mcp/CLAUDE_CODE.md — claude mcp add command
- docs/mcp/CLAUDE_DESKTOP.md — Settings > Integrations (NOT JSON config!)
- docs/mcp/CLAUDE_COWORK.md — remote + local bridge paths
- docs/mcp/PERPLEXITY.md — Perplexity Computer connector setup
- docs/mcp/CHATGPT.md — coming soon (requires OAuth 2.1, P0 TODO)
- docs/mcp/ALTERNATIVES.md — Tailscale Funnel + ngrok self-hosted options

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* chore: bump version and changelog (v0.6.0)

GBrain v0.6.0: Remote MCP server via Supabase Edge Functions + 12 bug fixes.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* docs: add Remote MCP Server section to README

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* docs: make document-release mandatory in CLAUDE.md, add MCP key files

Post-ship requirements section: document-release is NOT optional. Lists every
file that must be checked on every ship. A ship without updated docs is incomplete.

Also adds remote MCP server files to Key files section.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: batch upsertChunks into single statement to prevent deadlocks

The per-chunk UPSERT loop caused deadlocks under parallel workers because
each INSERT ON CONFLICT acquired row-level locks sequentially. Multiple
workers upserting different pages could deadlock on the shared unique index.

Fix: batch all chunks into a single multi-row INSERT ON CONFLICT statement.
One round-trip, one lock acquisition. COALESCE preserves existing embeddings
when the new value is NULL.

Fixes CI failure: "E2E: Parallel Import > parallel import with --workers 4"

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: advisory lock in initSchema() prevents deadlock on concurrent DDL

When multiple processes call initSchema() concurrently (e.g., test setup +
CLI subprocess, or parallel workers during E2E tests), the schema SQL's
DROP TRIGGER + CREATE TRIGGER statements acquire AccessExclusiveLock on
different tables, causing deadlocks.

Fix: pg_advisory_lock(42) serializes all initSchema() calls within the
same database. The lock is session-scoped and released in a finally block.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: add explicit test timeouts for CLI subprocess E2E tests

CLI subprocess tests (Setup Journey, Doctor Command, Parallel Import)
spawn `bun run src/cli.ts` which takes several seconds to JIT compile +
connect. The Bun test framework default 5000ms per-test timeout is too
tight for CI. Added 30-60s timeouts matching each subprocess's own
timeout to prevent false failures.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: infinite recursion in config.ts exported getConfigDir/getConfigPath

The replace_all refactor created recursive functions: the exported
getConfigDir() called the private getConfigDir() which called itself.
Renamed exports to configDir()/configPath() to avoid shadowing.

Also adds scripts/smoke-test-mcp.ts — verified all 8 MCP tool calls
work against a real Postgres database.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
2026-04-10 15:23:00 -10:00

12 KiB

CLAUDE.md

GBrain is a personal knowledge brain. Postgres + pgvector + hybrid search in a managed Supabase instance.

Architecture

Contract-first: src/core/operations.ts defines ~30 shared operations. CLI and MCP server are both generated from this single source. Skills are fat markdown files (tool-agnostic, work with both CLI and plugin contexts).

Key files

  • src/core/operations.ts — Contract-first operation definitions (the foundation)
  • src/core/engine.ts — Pluggable engine interface (BrainEngine)
  • src/core/postgres-engine.ts — Postgres + pgvector implementation
  • src/core/db.ts — Connection management, schema initialization
  • src/core/import-file.ts — importFromFile + importFromContent (chunk + embed + tags)
  • src/core/sync.ts — Pure sync functions (manifest parsing, filtering, slug conversion)
  • src/core/storage.ts — Pluggable storage interface (S3, Supabase Storage, local)
  • src/core/supabase-admin.ts — Supabase admin API (project discovery, pgvector check)
  • src/core/file-resolver.ts — MIME detection, content hashing for file uploads
  • src/core/chunkers/ — 3-tier chunking (recursive, semantic, LLM-guided)
  • src/core/search/ — Hybrid search: vector + keyword + RRF + multi-query expansion + dedup
  • src/core/embedding.ts — OpenAI text-embedding-3-large, batch, retry, backoff
  • src/mcp/server.ts — MCP stdio server (generated from operations)
  • supabase/functions/gbrain-mcp/index.ts — Remote MCP server (Supabase Edge Function)
  • src/edge-entry.ts — Curated bundle entry point for Edge Function (excludes fs-dependent modules)
  • src/commands/auth.ts — Standalone token management (create/list/revoke/test)
  • 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)
  • scripts/deploy-remote.sh — One-script remote MCP deployment
  • docs/mcp/ — Per-client setup guides (Claude Desktop, Code, Cowork, Perplexity, ChatGPT)
  • openclaw.plugin.json — ClawHub bundle plugin manifest

Commands

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

Testing

bun test runs all tests (20 unit test files + 4 E2E test files). 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/sync.test.ts (sync logic), 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/doctor.test.ts (doctor command), 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), 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).

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)
  • test/e2e/upgrade.test.ts runs check-update E2E against real GitHub API (network required)
  • 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.
  • Always run E2E tests when they exist. Do not skip them just because DATABASE_URL is not set. Start the test DB, run the tests, then tear it down.

API keys and running ALL tests

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

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.

  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:
    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. Run E2E tests: DATABASE_URL=postgresql://postgres:postgres@localhost:PORT/gbrain_test bun run test:e2e
  5. 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.

Skills

Read the skill files in skills/ before doing brain operations. They contain the workflows, heuristics, and quality rules for ingestion, querying, maintenance, enrichment, and setup. 7 skills: ingest, query, maintain, enrich, briefing, migrate, setup.

Build

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

Pre-ship requirements

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

  • 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.

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 voice

CHANGELOG.md is read by agents during auto-update (Section 17). The agent summarizes the changelog to convince the user to upgrade. Write changelog entries that sell the upgrade, not document the implementation.

  • 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"

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.

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:

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.

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