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Garry TanandClaude Fable 5 d35c9c9e44 v0.45.0.0 feat(bootstrap): paste-in personal-agent install for Codex + Claude Code (#3975) 
* docs(designs): agent-bootstrap plan + design docs (normative, review-absorbed)

The scrubbed, in-repo sources of truth for the gbrain bootstrap wave:
AGENT_BOOTSTRAP_DESIGN.md (product scope/sequencing) and
AGENT_BOOTSTRAP_PLAN.md (implementation; all review-finding IDs inlined).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): format spec, question bank, identity templates, bundled assets

agent.json manifest (format_version 1, initialized sentinel) + machine-local
install receipt [CX2-1, CX2-12]; 12-question/6-required interview bank with
consent keys and a persist:false sink for the optional provider key [CX2-13];
ten {{TOKEN}} identity templates (generic, adapted to gbrain ops — gates call
recall/query/put_page, write-through-ops rule, keyless agent-authored facts,
silence contract); assets embedded compiled-binary-safe via file-type imports
[ENG-6].

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): runbook, README paste block, bootstrap guide, TODOS entries

BOOTSTRAP_FOR_AGENTS.md (agent-driven install runbook: CLI phase list is the
source of truth, never-invent rules, Codex approvals preflight, keyless posture,
failure-modes table, version stamp for the skew check); README gains the
full-agent paste block pinned to latest-stable inside the Claude Code/Codex
quick start (memory-only tier stays); docs/guides/bootstrap.md carries the full
install/security/consent/degradation/uninstall contract.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(designs): spike instrument for the bootstrap wave (build order 0)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): interview + render engines

Interview gate with read-back confirm-hash (any later answer change clears the
confirmation — the hostile single-batch case is structurally impossible),
per-answer provenance, caps + escaping at set time, config-sink routing for the
provider key; renderer with hard-fail token sweep, subordinate fencing of
principal input, never-clobber + backups, deterministic minimal mode for the
template repo, scaled byte floors. 58 unit tests.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): private-repo lifecycle — repo create, attach, uninstall, run lock

gh-gated private repo creation with API-verified privacy (rate-limit distinct
from public), refuse-foreign-origin with attach as the sanctioned path, atomic
bootstrap mutex (pid liveness + age + token), receipt-keyed uninstall that
never wholesale-deletes the gbrain home and only offers --delete-brain for a
brain it created; read-only PGLite lock probe (never opens the engine).
54 unit tests, injectable exec seam throughout.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(release): latest-stable ref, template-repo publish job, bootstrap CI guards

release.yml advances the latest-stable tag only after assets publish (the paste
block's permanent ref — copies in the wild never rot) and gains a PAT-gated
publish-template job verified against the vendored tree; two skip-graceful
guards (sanctioned-ref + runbook stamp; template/token bijection + placeholder
assertion + generator byte-diff) wired into verify; README + runbook re-admitted
to the CI cache hash; vendored deterministic template tree generated.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(context): IPC v2 turn_context + 8KB assembly + visibility resolver + session identity

Discriminated-union IPC with handler map, protocol echo (stale-serve detection),
shared-secret gate, server-side source binding, per-kind budgets; turn-context
assembly (reflex pointers + volunteered pages + world-only hot facts) under a
data-not-instructions envelope trimmed to the harness's 10KB hook-output cap;
facts.default_visibility resolved through one helper at all four sites (explicit
caller wins, typos fail closed); typed sessionId threads _meta.session_id into
the hot-memory cache key. 50 new tests; 180 adjacent tests confirmed green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(persistence): secret-scan, gbrain sources push, durability unification

Pattern secret scanner (own runtime allowlist, redacted previews, corpus-write
redaction mode); sources push runs the whole scan→stage→commit→pull→push
sequence under one cross-platform lock (mkdir-atomic, pid+age+token) with a
deny-glob backstop, commit-first divergence-safe pull, refuse-unverifiable
visibility, and push-status telemetry; gbrain-home choke point unifies
GBRAIN_HOME semantics with config (0700); durability is parent-repo-aware and
rotates its push log at 0600. 35 new tests; 200 existing green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(sources): harden/pull gates accept sources inside a parent git repo

The bootstrap workspace registers brain/ (a subdirectory) as the source; the
durability core already resolves the repo root, so the command gates now check
inside-a-repo rather than .git-right-here [CX2-3].

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(serve): resident maintenance sweep + keyless capability probe

The lock-owning serve process now closes the persistence loop: startup (3s
post-connect, best-effort, unref'd) and idle (10-min quiet intervals through
the injectable timer seam) sweeps run facts-fence reconciliation, deterministic
link/timeline extraction over recent workspace pages, and spend-gated corpus
ingest (skipped keyless — agent-authored fences cover it). gbrain sweep --once
is the trusted CLI seam bootstrap verify uses. Capability probe renders the
honest keyless/keyed report. Full reuse of the cycle extractor + extract cores;
26 new tests, neighbors green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(hooks): engine-free gbrain hook command, settings writers, transcript parser

Four hook events (session-start digest + crashed-session recovery push,
user-prompt turn-context injection under an 800ms deadline and the 10KB cap,
stop buffers, session-end corpus write with redaction/retention/dedup +
best-effort push); structural JSON settings merger keyed by a _gbrain marker
(foreign hooks and permissions survive); dated host-spec registry; Claude Code
.jsonl parser as a spec-target with a scrubbed 7-shape fixture. Heartbeat is
counters-only by construction. 59 tests; zero engine modules in the import
graph.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(bootstrap): cross-link the full-agent path from the connection docs

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): dispatcher, verify, status — the command assembled

gbrain bootstrap {status,interview,render,repo,hooks,verify,uninstall,attach}:
engine-free except verify (owns its engine, in-process sweep — no live-serve
conflict); phase list is the TS source of truth with install.jsonl telemetry
and the support blob; verify's fail-soft check suite covers the real write path
(put_page → write-through file → sweep → graph floor → recall), passes keyless,
persists snapshots, and ends with the first-run tour. cli.ts wired per the
three-touchpoint rule; doctor gains the bootstrap check group (silent on
machines with no bootstrap state). 28 new tests; 353 adjacent green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs: KEY_FILES bootstrap cluster + CLAUDE.md dispatcher row (+ build:llms)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(bootstrap): e2e pins — hook-under-live-serve, attach, degraded modes, compiled binary, Docker harness

The permanent pins: a real serve holds the PGLite lock while the engine-free
hook completes (and a direct engine open provably throws LiveServeLockError);
stale-socket fail-open; machine-2 attach with marker-keyed hook repair;
decline-everything installs verify green with every degradation named; the
compiled binary renders bundled templates in an empty cwd. Offline Docker
harness (networkless, read-only) gated into heavy-tests.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(bootstrap): register doctor check categories + system-of-record allow comments

The six bootstrap doctor checks join OPS_CHECK_NAMES; the sweep's batch link/
timeline inserts carry the explicit extract-path allow comments (the sweep IS
the extraction path for workspace pages).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(test): shard wedge cap tracks suite growth (1500s -> 1800s)

At ~9000 tests a healthy shard finished at 1466s and two progressing shards
were false-killed at the old cap; 1800s restores ~25% headroom over the
slowest observed healthy shard. Real hangs still hit it.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(ci): cache-hash policy — README + runbook edits must invalidate [C2]

The old deny-list assertion predates the paste block; README.md and
BOOTSTRAP_FOR_AGENTS.md are policy-doc re-admissions now, so their edits must
change the hash (a paste-block edit shipping under a cached green was the C2
hole).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(test): classify post-suite exit-hangs as warn-pass; file the leak forensics

A shard killed by the wedge watchdog with every assigned file started and zero
fail markers did all its work and leaked a handle at exit — pre-existing and
master-reproducible (P1 TODO carries the full bisect forensics). Bun's per-test
timeout turns a hung test into a (fail), so the classifier cannot mask one.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(test): shard cap 2400s — the count-balanced heavy shard needs it under contention

Observed: the heavy shard still progressing 22s before an 1800s kill while
siblings finish at 1150-1550s (split balances file count, not weight). Filed
the load-sensitive WAL-repair flake (pre-existing, master's v0.42.75.0 wave).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(bootstrap): quarantine env-mutating suites to the serial lane

check-test-isolation R1: six new files mutate GBRAIN_HOME/env at module scope —
the serial lane (one process per file) is the guard's prescribed home for them.
All 114 tests pass post-rename.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(readme): per-harness install sections — Codex, Claude Code, then OpenClaw/Hermes

Each harness gets its own complete paste-block section (desktop app first,
terminal noted — Claude Code CLI is the identical harness; Codex CLI works
pull-based today); the OpenClaw/Hermes platform path keeps equal weight with
its one-click deploys and INSTALL_FOR_AGENTS block intact; memory-only and
remote-connect tiers consolidated under 'Lighter ways in'. Supersedes the
review's D5 ordering by user direction; stale heading references updated.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(readme): Codex as the recommended first step; OpenClaw/Hermes framed as-intended, high-cost

The install section now routes newcomers explicitly: Codex first
(subscription-priced, nothing to deploy), OpenClaw/Hermes as GBrain used the
way it was designed — always on, at real server + API cost.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix: doc-audit code chasers — broken recovery hints, stale op description, auto_link key

Four small code fixes surfaced by the markdown accuracy audit:
- doctor's auto-RLS recovery hint pointed at `apply-migrations --force-retry 35`,
  which cannot work (--force-retry targets the vX.Y.Z orchestrator registry, not
  the numeric schema MIGRATIONS array). Hint now points at the recreate SQL in
  docs/guides/rls-and-you.md; test pins against regression.
- v0_11_0 migration printed the same broken-mechanism class of hint
  (`config set minion_mode` writes DB config nothing reads); now names
  `apply-migrations --mode` + preferences.json, the real setter.
- submit_job's op description hardcoded a stale handler list; now points at
  registerBuiltinHandlers as the source plus the --follow discovery trick.
- `auto_link` added to KNOWN_CONFIG_KEYS: read by link-extraction, reconcile-links,
  and sweep, and documented as the off-switch in brain-ops/maintain, but the
  allowlist rejected `config set auto_link false`.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs: repo-wide accuracy + MECE reform from the 9-bucket markdown audit

A code-grounded audit of every markdown file (root, architecture, guides,
mcp, tutorials, docs-root, operations/eval/designs, skills, recipes) followed
by a fix wave with per-bucket ownership. Four classes of change:

Accuracy — every documented command/flag verified against src/ before writing:
dead commands replaced with working ones (pages purge-deleted, jobs watch
--follow, gbrain restore, import-based Obsidian flow, space-separated --scopes,
real thin-client recipes, working isolation verification, real supervisor
restart procedure, curl-based ngrok health check, real minion_mode setter);
count drift fixed with rot-proof phrasing (100+ ops, 50+ bundled skills via
skills/manifest.json, 140+ engine methods, KNOBS_HASH_VERSION pointer instead
of hardcoded versions); stale claims corrected (search-mode defaults, RETRIEVAL
pipeline order incl. autocut, sentinel rules, refusal-list mechanism, engine
snapshot, shard cap 2400s + EXIT-HANG classifier in TESTING.md, latest-stable +
publish-template documented in RELEASING.md as release.yml promises).

MECE — one home per concept, pointers elsewhere: test isolation → TESTING.md;
OAuth registration + --bind/--public-url lore → DEPLOY.md; mode bundles →
guides/search-modes.md (the home the CLAUDE.md dispatcher always promised);
merge contract → schema-packs.md; WAL ladder → ENGINES.md; quiet-hours →
quiet-hours.md; capture taxonomy → entity-detection.md; person-page taxonomy →
compiled-truth.md; brain-first protocol → brain-first-lookup.md; refresh
semantics → refresh-algorithm.md; KEY_FILES.md deduplicated (58 extension
entries merged, one entry per file); infra-layer.md rewritten as a pointer page.

Privacy — placeholder sweep across guides, docs, skills, and recipes per the
iron rule; per-release narration stripped from reference docs (current-state
prose only).

Bootstrap coverage — AGENTS.md pointer, RESOLVER routing row, INSTALL.md path,
tutorial cross-links, keyless-mode sections in spend-controls/headless-install.

skills.lock.json regenerated; llms.txt/llms-full.txt rebuilt. Gates: verify
36/36, typecheck clean, doctor 96/96, skills-integrity + resolver + build-llms
+ config-set + migrations all green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs(readme): refresh production-brain stats to current brain-repo counts

155,795 pages / 24,589 people / 5,340 companies, counted from the brain
repo's current HEAD; the "100K-page brain" framing moves to 150K to match.
Cron-fleet count unchanged (its store lives on the deployment host, not in
the repos available for verification).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(scan,push): modern OpenAI/Voyage key patterns, scan staged blobs not disk

- secret-scan matches sk-proj-/sk-svcacct-/sk-None- and pa- Voyage keys
  (the bare sk- pattern missed every current OpenAI key format).
- workspacePush stages first, then scans the staged index blobs via
  git cat-file, closing the scan-then-stage TOCTOU where a file changed
  between snapshot and commit shipped unscanned.
- shared binary-sniff helper, memoized glob regexes, atomic push-status
  write, and tests for pull_conflict + gitignored deny-match paths.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ci): regenerate flag registry for new commands, harden shard classifier + release token

- cli-flag-registry.generated.ts regenerated: bootstrap/hook/sweep and
  sources push --message/--allow-unverified-remote were missing, so the
  strict #2185 validator rejected real invocations and skipped the new
  commands entirely.
- EXIT-HANG shard classifier now requires every assigned file to have
  started before warn-passing a watchdog kill (was fail-open).
- release.yml passes TEMPLATE_REPO_PAT via http.extraheader, off the argv.
- compiled-binary e2e fails loud in CI instead of a silent permanent skip.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(hook,sweep,ipc): non-blocking hook pushes, bounded sweep + cache, source-bound resolve

- session-start/session-end no longer run synchronous git + inline push
  inside their self-deadline; a detached child does the push and the hook
  returns immediately (blocked Claude Code startup for minutes on a dirty
  tree before).
- serve sweep drops the unbounded listAllPageRefs, resolves only candidate
  targets, claims corpus files atomically (no double-LLM-spend race), and
  caps the fence LIKE scan; heartbeat writes are O_APPEND with rare compaction.
- hot-memory cache evicts expired entries and bounds entry count (the key is
  caller-controlled via _meta.session_id).
- v1 resolve IPC honors boundSourceId like turn_context; turn-context runs
  its arms concurrently. doctor reads push/heartbeat thresholds from hook.ts.
- new tests: doctor bootstrap checks, hook push-gate + deadline, concurrent
  sweep claims, cache eviction, bound-source resolve.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(bootstrap): origin-ownership gate, world visibility, collision-safe source id, consent + templates

- repo adoption requires an exact receipt repo_url match or authed-owner
  check (undefined repo_url was a wildcard); create verifies privacy BEFORE
  the first push.
- verify sets facts.default_visibility=world if unset, so agent-authored
  facts surface in per-turn context (they defaulted private before).
- source_id derives a path-hash suffix when 'workspace' is taken by another
  checkout; every consumer reads manifest.source_id.
- skipped HOOKS_CONSENT now declines (was falling through to default yes);
  --minimal refuses on an initialized manifest; tilde fences escaped.
- MCP registration pins --surface full; status hard-fails a public origin
  (template door); receipt writers guard against newer/corrupt receipts;
  uninstall only claims brain-deleted after a real rm.
- templates ship jobs disabled + provider-consent + support-relay lines;
  soul-audit re-runs over the shared interview bank. TODOS: 11 follow-ups.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(security): close adversarial-review findings — scan fails closed, whole-PEM redaction, bound repo push

Cross-model adversarial pass (Claude + Codex) on the bootstrap wave:

- secret scan fails CLOSED: an unreadable, oversized, or binary staged blob
  now blocks the push (blocked_unscannable, exit 5) instead of committing
  unscanned; only a confirmed staged deletion is skipped. This was the
  headline "block secrets before they leave the machine" property failing open.
- private-key redaction spans the whole PEM block (header+body+footer), not
  just the header line — the base64 body no longer survives into the corpus
  the sweep sends to an extraction provider.
- bootstrap repo commits the workspace (secret-scan-gated) before the first
  push and verifies the remote actually received it, so a push-fail retry
  can't adopt an empty remote as success.
- privacy verify is re-bound to origin immediately before push (a concurrent
  origin rewrite between verify and push is refused).
- session-end corpus write is atomic and clears the stale ingested/in-progress
  sidecars so a resumed session's appended transcript is re-ingested.
- public-origin refusal enforced at render (not only status); MCP "already
  registered" is verified to target this workspace, not blessed blindly;
  verify probe cleanup scopes deletes to its own slugs, not a token substring;
  allowlist fingerprint floor raised 8→16 hex.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* v0.45.0.0 feat(bootstrap): paste-in personal-agent install for Codex + Claude Code

Turns a Codex or Claude Code session into a persistent personal agent:
interview-rendered identity files, a local PGLite brain, per-turn context via
serve IPC (Claude Code hooks / Codex pull protocol), session-triggered
persistence, and a private GitHub repo as the agent's portable body. Keyless-
first (the harness model is the LLM; one optional key adds embeddings +
extraction). New `gbrain bootstrap` command family + `gbrain hook` + `gbrain
sweep`; doctor bootstrap health checks; latest-stable distribution ref +
template-repo publish job. Opt-in, additive — existing installs untouched.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix: regenerate flag registry for security-fix flags; drop fabricated gbrain capabilities doc ref

CI caught two real failures under the merged state:
- the flag registry lagged the blocked_unscannable/exit-5 flags the security
  round added, tripping the #2185 freshness guard.
- headless-install.md described the keyless capability report as a
  `gbrain capabilities` command, which the #3502 doc-command resolver
  rejects — reworded to prose (the real surface is bootstrap verify's report).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* docs: sync KEY_FILES + bootstrap plan to security-fix behavior

Cross-referenced the security-fix round against the reference docs and
corrected the drift those commits introduced:

- workspace-push.ts entry: stage-FIRST-then-scan order (the TOCTOU fix),
  fail-closed blocked_unscannable, and the sources-push status -> exit-code map.
- hooks.ts entry: MCP registration pins `serve --surface full`.
- hook.ts entry: session-start/session-end pushes run in a detached child
  (non-blocking); atomic corpus write clears stale sidecars.
- bootstrap.ts entry: render hard-refuses a public origin (template door).
- verify.ts entry: source_id collision resolution (workspace-<path-hash>).
- AGENT_BOOTSTRAP_PLAN as-shipped delta note for the scan/stage reorder.

llms bundle unchanged (KEY_FILES is link-only); build:llms and
test/build-llms.test.ts green.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ci): silence SC2016 on the intentional askpass literal in release.yml

The one-shot GIT_ASKPASS script must contain literal $1 and
$TEMPLATE_REPO_PAT so they expand when /bin/sh runs it at git's credential
prompt, not when the outer shell writes the file — single quotes are correct.
Add a scoped shellcheck disable so actionlint passes.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(skills): declare 'bootstrap my data' trigger in cold-start frontmatter

The doc reform added 'bootstrap my data' to cold-start's RESOLVER.md row (to
disambiguate data-bootstrap from agent-bootstrap) but not to the skill's own
frontmatter triggers, tripping the RESOLVER↔frontmatter round-trip contract
(resolver.test.ts). Declare it; regenerate skills.lock.json.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* feat(bootstrap): default per-turn hooks + search mode ON without a prompt

Installing gbrain for your coding agent IS the consent for the behaviors that
make it work, so stop re-litigating them with install-time questions whose
"no" defeats the product:

- Per-turn hooks (Claude Code) install ON by default — no prompt. Off-ramps:
  `--no-hooks` at install, `GBRAIN_HOOKS=0` at runtime, `bootstrap uninstall`.
  The "hooks installed" line now surfaces the kill switch so default-on is
  never silent. A persisted HOOKS_CONSENT=no (interview --skip) still declines.
- Search mode defaults to `balanced` silently (nobody knows the modes at
  install; `gbrain search modes` changes it any time).
- MCP scope stays the ONE deliberate prompt — project vs user is a real
  cross-repo privacy choice, not friction.

Marks the two consents `silent: true` in the question bank (new QuestionSpec
field), rewrites the runbook phases so the agent no longer asks them, adds the
`--no-hooks` flag (+ registry regen), and adds default-on / opt-out tests.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(bootstrap): real end-to-end coverage — cross-session recall, per-turn content, Codex door, realistic corpus

Closes the seven e2e gaps a coverage audit surfaced: the plumbing was
well-unit-tested but the product claims ("Codex works, context shows up every
turn with real content, it remembers across restarts, machine two recovers,
Postgres works") were unproven end to end. Test-only wave — zero src changes.

- Hermetic synthetic corpus (test/fixtures/bootstrap-corpus/ + a loader helper):
  12 interlinked pages (52 edges, timelines), 12 world/private beliefs, 8 gold
  queries — curated from the gbrain-evals synthetic corpora, 100% placeholder
  names, so recall is asserted on a real multi-entity brain instead of a
  2-node self-planted probe.
- GAP1 magic moment: author a fact via the real write path, disconnect the
  engine, reopen against the same DB, recall it — a real session boundary, not
  verify.ts's same-connection SQL read-back. Plus a source-isolation assertion.
- GAP2 per-turn content: hook-under-serve Pin 1 now seeds a known fact and
  asserts its text lands in the injected block AND private beliefs never do
  (was: empty brain, empty_block accepted as a pass).
- GAP3 Codex door: assert the rendered AGENTS.md carries the Gate-3 brain-first
  pull protocol; make the fake codex shim implement `mcp get` so the [FIX7]
  target-verification can actually fail; the Docker cold-machine harness now
  exercises the hooks/MCP registration step instead of skipping it.
- GAP4 corpus recall: turn-context + verify graph-floor/qrels run on the real
  multi-entity brain with real edges.
- GAP5 attach: machine-two now re-ingests the cloned brain/ into a fresh DB and
  recalls a fact authored only on machine one — the multi-device payoff.
- GAP6 keyed + Postgres (env-gated): real embeddings prove semantic recall a
  paraphrase query can reach but keyless BM25 cannot; bootstrap verify drives a
  real Postgres engine (skipIf DATABASE_URL/keys absent).
- GAP7 persistence: session-end runs the REAL push (not the mocked seam) to a
  local bare remote and the remote receives the content; a planted secret is
  blocked at the gate; the 15-min cron installs and fires a scan-gated push.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* test(bootstrap): real-agent e2e — drive the actual claude + codex binaries end to end

Closes the audit's biggest gap ("no real harness ever drives a turn"). Adapts
gstack's PTY/headless agent harness to prove the bootstrap install + smoke work
against the REAL binaries, not PATH shims. Test/CI/docs only — zero src changes.

- test/helpers/agent-harness.ts: hermetic clean-room child env (ported from
  gstack; drops CONDUCTOR_/CLAUDE_/GSTACK_/MCP_/GBRAIN_, promotes
  GSTACK_ANTHROPIC_API_KEY→ANTHROPIC_API_KEY), real-binary resolvers + auth
  probes, headless `claude -p --output-format stream-json` and `codex exec
  --json` turn runners, a gbrain stdio MCP-config writer, and a keyless brain
  seeder. + a fixture-parse unit test (no binary needed).
- test/e2e/bootstrap-real-claude.serial.test.ts: real `gbrain bootstrap`
  install → REAL `claude mcp add` (verified via `claude mcp get`) → verify
  exit 0 → a real `claude -p --mcp-config --strict-mcp-config` turn that
  invokes mcp__gbrain__search and answers from the brain (proven: toolCalls
  include mcp__gbrain__search, final text carries the seeded fact).
- test/e2e/bootstrap-real-codex.serial.test.ts: same install with REAL `codex
  mcp add` into a real ~/.codex/config.toml + Gate-3 pull-protocol assertion,
  then a real `codex exec --json` turn surfacing the fact (MCP or the pull-
  protocol shell path). Bounded retry absorbs codex's occasional MCP-call
  cancellation without softening the fact-requiring assertion.
- Everything hermetic (temp HOME/CLAUDE_CONFIG_DIR/CODEX_HOME/GBRAIN_HOME;
  real ~/.codex auth copied read-only) and skipIf-gated so it self-skips
  cleanly where the binaries/auth are absent.
- heavy-tests.yml: gated `real-agent-e2e` job (nightly/label, never the PR
  shard; no-op on a runner without authed binaries).
- TODOS: compiled `gbrain` binary can't serve a PGLite brain (bun compile
  omits the WASM/extension payloads); harness falls back to `bun run` serve.

Verified against live claude 4.6 + codex 0.147.0: 15 pass / 0 fail; verify
36/36; typecheck clean.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(ci): real-agent-e2e job — bash array + --timeout (actionlint SC2086 + bun-test-timeout guard)

The real-agent-e2e job's file loop used an unquoted $FILES (SC2086) and ran
`bun test` without --timeout (check-bun-test-timeout guard). Switch to a bash
array and add --timeout=600000 (real-agent turns are slow; the tests self-skip
without authed binaries so it's a no-op elsewhere).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(pglite): embed WASM + extension assets so the compiled binary can serve

A `bun build --compile` gbrain binary could not `serve` a PGLite brain: the
compile bundles JS but not PGLite's runtime payload (pglite.wasm, initdb.wasm,
pglite.data, vector/pg_trgm tarballs), so `serve` on PGLite died with a
bunfs/ENOENT. Now the assets ride inside the binary.

- src/core/pglite-embedded-assets.ts: embeds the five assets via
  `import … with { type: 'file' }` (the ENG-6 idiom) and exposes
  getEmbeddedPgliteOptions() → { pgliteWasmModule, initdbWasmModule, fsBundle,
  extensions:{vector,pg_trgm} }. WASM/fsBundle are consumed as bytes; the two
  extension tarballs are materialized to a content-addressed temp file (atomic,
  size-verified reuse) because PGLite reads them via fs.createReadStream, which
  cannot read a /$bunfs path. Unconditional (works in bun-run and compiled),
  so no fragile mode branch.
- src/core/pglite-engine.ts: static-import getEmbeddedPgliteOptions (engine
  path stays static per the engine-dynamic-import invariant); spread into both
  PGlite.create sites (initial + WAL-repair retry). The bunfs classifier stays
  as a backstop but no longer fires for a correct binary.
- scripts/check-pglite-embedded.sh (+ smoketest): compiles a focused binary and
  asserts it boots PGLite, CREATE EXTENSION vector/pg_trgm, and round-trips a
  page — wired into `bun run verify` (now 37 checks), check:all, and
  check:pglite-embedded. Fail-soft only when compile is unavailable.
- agent-harness.ts probeCompiledPglite now passes → the real-agent e2e uses the
  fast compiled MCP server. TODOS: the P2 "can't serve PGLite" item is closed.

Verified: fresh compiled binary ran `search`/`query` against a PGLite brain and
returned the seeded row (no bunfs/ENOENT); verify 37/37; pglite-engine 120/0
source-mode; typecheck clean; engine-dynamic-import + parity guards pass.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-08-11 16:42:11 -07:00
Garry Tan f07e9dff11 fix(ci): release build gates on the artifact, not a serial re-run of the whole suite 
The first Release run (30698650484) failed before building anything: the
build job re-ran the entire unit suite serially on the release runner —
a different environment from the sharded Test workflow that had already
gated the exact SHA at merge — and died on ambient-env tests. The review
of #3573 predicted this ('a flaky test now blocks the release'). The
build job now compiles and smoke-tests the binary (--version must match
the VERSION file), which validates the actual artifact — something the
test suite never did. The Test workflow remains the code gate.
 2026-08-01 20:43:58 +08:00
Garry Tan 0244104b8d fix(ci): env-bind the release-notes version interpolation 
Review hardening from the #3573 gatekeeper pass: a ${{ }} inside run: is
shell injection by construction; bind through env instead. Not
attacker-reachable today (VERSION comes from master), correct anyway.
 2026-08-01 19:55:28 +08:00
Garry TanandTime Attakc 48618bd4bf feat(ci): publish GitHub releases so binary self-update can work (#3521) (#3573) 
Co-Authored-By: Time Attakc <89218912+time-attack@users.noreply.github.com>
 2026-08-01 19:55:28 +08:00
Time AttakcGarry TanClaude Opus 5
 		913d2d7f79 fix(test): give slow setup hooks a real timeout budget (#3566) 
bun ignores bunfig.toml's timeout key, and beforeAll/beforeEach hooks do
NOT inherit a test's third-arg timeout — a bare `bun test` gives every
hook the 5000ms default even when all tests in the file declare 30s+.
Measured on bun 1.3.14: a 6s hook dies at ~5001ms with the signature
`(unnamed) [5001ms] ... hook timed out` (the #3545 jsonb-parity CI
failure); both `beforeAll(fn, ms)` and the CLI `--timeout` flag are
enforced hook budgets (kills observed at exactly the configured ms).

Fixes:
- e2e.yml (jsonb-parity, tier1, tier2) and release.yml ran bare
  `bun test`; they now pass --timeout=60000 like every scripts/ runner.
- test/e2e/jsonb-roundtrip.test.ts (the #2339 double-encode guard, which
  only real Postgres can surface) additionally carries per-hook 60s
  budgets so a bare local run can't flake either — same pattern as its
  sibling op-checkpoint-jsonb-parity.test.ts.
- scripts/check-bun-test-timeout.sh: CI guard (run from test.yml's
  verify job) failing any future bare `bun test` in workflows/scripts.
- scripts/run-e2e.sh: correct the comment claiming --timeout is
  per-test-only (it covers hooks; the outer gtimeout exists for
  sync-blocking WASM hangs where no timer can fire).

Proof: with Postgres paused for 6s during setupDB's connect, the
unfixed file fails at 5001.81ms with the exact CI signature; the fixed
file passes the identical condition (5 pass, 6.57s). 396 slow
before-hooks across 362 test files lack per-hook budgets; all of them
run through --timeout-passing invocations after this change, enforced
by the new guard.

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
 2026-07-28 20:08:36 -07:00
Time AttakcGarry TanClaude Fable 5
 		800108e014 v0.42.65.0 chore(release): 93 verified fixes since v0.42.64.0 — changelog + version bump (#3346) 
* chore(ci): refresh GitHub Actions SHA pins (checkout v4, action-gh-release v2)

Pre-ship pin staleness check per docs/RELEASING.md: both floating major
tags moved upstream; pins updated to the current tag commits.

* v0.42.65.0 chore(release): 92 verified fixes since v0.42.64.0 — changelog + version bump

Aggregates everything merged to master since the v0.42.64.0 bump commit:
community fixes, credited takeovers, batch re-lands, CI hardening, and
maintainer-approved features. Net commit list excludes revert pairs.
No new schema migrations.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* fix(deps): clear OSV-flagged transitive dependencies via override floors

Raise the existing security-floor overrides so the lockfile resolves
patched versions of three transitive packages flagged by the OSV scan
(@hono/node-server, fast-uri, body-parser). None are on gbrain's own
runtime path (@hono/node-server is only referenced by the MCP SDK's
optional hono transport, which gbrain does not load); the floors keep
the dependency scan green. MCP/OAuth unit tests pass against the
resolved versions.

* chore(release): fold #3110 into the v0.42.65.0 entry (93 net changes)

---------

Co-authored-by: Garry Tan <garrytan@gmail.com>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-07-23 16:45:29 -07:00
Time AttakcSinabinaClaude Fable 5
 		9aaa3be05f ci(security): OSV dependency scan, release artifact attestations, Semgrep CE SAST (#2182 #2142 #2272) (#2917) 
Co-authored-by: Sinabina <sinabina@Sinabinas-MacBook-Pro-4.local>
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
 2026-07-17 11:05:13 -07:00
mzkarami 414940204a ci(release): run verify before build (#2243) 2026-07-16 20:47:35 -07:00
Garry TanandClaude Opus 4.7 d28be5d091 v0.40.4.0 feat(search): selective graph signals + per-stage attribution + audit-writer unification (#1300) 
* v0.40.4.0 T1: shared audit-writer primitive

Extract createAuditWriter() helper. Five hand-rolled JSONL audit
modules (rerank-audit, shell-audit, supervisor-audit, audit-slug-
fallback, phantom-audit) duplicated the same ISO-week filename math,
best-effort write loop, and read-current-plus-previous-week loop.
T2 refactors all 5 onto this primitive.

Behavior preservation: filename format, JSONL line shape, mkdir
recursive, appendFileSync utf8, stderr-on-failure all byte-identical
to the existing modules so their tests pass unchanged.

resolveAuditDir() moves here from shell-audit.ts; shell-audit.ts
will re-export for back-compat (T2). Honors GBRAIN_AUDIT_DIR with
whitespace-trim, falls back to ~/.gbrain/audit/.

Test coverage: 22 cases covering ISO-week math + year-boundary edges
(2027-01-01 → 2026-W53), env override, mkdir-recursive, fail-open
stderr-warn shape, cross-week readback, corrupt-row skip, non-finite-
ts skip, round-trip with nested fields, computeFilename + resolveDir
accessors.

Plan ref: D5=B audit unification cathedral expansion.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T2: refactor 5 audit modules onto shared writer

Replace the duplicated ISO-week filename math + best-effort write loop
+ read-current-plus-previous-week loop in:
  - src/core/rerank-audit.ts (rerank-failures-*.jsonl)
  - src/core/audit-slug-fallback.ts (slug-fallback-*.jsonl)
  - src/core/minions/handlers/shell-audit.ts (shell-jobs-*.jsonl)
  - src/core/minions/handlers/supervisor-audit.ts (supervisor-*.jsonl)
  - src/core/facts/phantom-audit.ts (phantoms-*.jsonl)

All five now delegate file I/O to createAuditWriter from T1. Public
API preserved bit-for-bit:
  - logRerankFailure, readRecentRerankFailures, computeRerankAuditFilename
  - logSlugFallback, readRecentSlugFallbacks, computeSlugFallbackAuditFilename
  - logShellSubmission, computeAuditFilename, resolveAuditDir
  - writeSupervisorEvent, readSupervisorEvents, computeSupervisorAuditFilename
    plus isCrashExit, summarizeCrashes, CrashSummary (domain-specific
    helpers stay in supervisor-audit.ts; only file I/O moves)
  - logPhantomEvent, readRecentPhantomEvents, computePhantomAuditFilename

Domain-specific behavior preserved:
  - audit-slug-fallback emits per-call stderr (D7 dual logging) in the
    caller; the shared writer is failure-only stderr
  - rerank-audit truncates error_summary to 200 chars before write
  - phantom-audit spreads optional fields conditionally (skip undefined)
  - supervisor-audit keeps single-file readback (no cross-week walk)
    to preserve pre-v0.40.4 doctor assertions

resolveAuditDir lives in src/core/audit/audit-writer.ts; shell-audit.ts
re-exports it so existing imports keep working (every other audit
module + gbrain-home-isolation.test.ts + minions.test.ts +
minions-shell.test.ts pull resolveAuditDir from shell-audit.ts).

Operator-visible drift: rerank-audit stderr line drops the
'rerank-failure audit' qualifier — was '[gbrain] rerank-failure audit
write failed (...)' now '[gbrain] write failed (...); search continues'.
Stderr is human-debugging, not machine-parsed; the file written gives
the qualifier away in `tail -f audit/*`.

Test coverage: 128/128 audit-touching tests pass unchanged.

Plan ref: D5=B audit unification cathedral expansion.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T3: getAdjacencyBoosts engine method (PG+PGLite parity)

Add BrainEngine.getAdjacencyBoosts(pageIds) returning Map<page_id,
AdjacencyRow{hits, cross_source_hits}>. Returns ALL pages with
hits >= 1 (callers apply their own threshold).

Cross-source semantic (D15=A): cross_source_hits EXCLUDES the target
page's own source. A page in source A linked from 2 pages in source A
reports cross_source_hits = 0. Linked from 1 in source B + 1 in
source C reports 2.

Source-scope contract: pageIds MUST already be source-scoped by the
caller. Method does NOT filter by source_id. The in-set restriction
makes cross-source leakage impossible by construction. JSDoc spells
this out; same trust posture as cosineReScore's chunk_id handling.

COALESCE(p.source_id, 'default') on both target and from-page sides
for defense-in-depth even though pages.source_id is NOT NULL today.

JSDoc/SQL contract alignment (codex #2): HAVING >= 1 matches the
"returns ALL pages with hits >= 1" contract; threshold of 2 is the
caller's call in applyGraphSignals.

Known limitation (codex #15): cross_source_hits cannot distinguish
"genuinely linked from another team" from "mirrored imports from
another source." T-todo-4 captures the v0.41+ refinement.

SearchResult type extension (D4=A flat fields, D12=A attribution):
  - graph_adjacency_hits, graph_cross_source_hits,
    graph_session_demoted, graph_session_prefix
  - base_score, backlink_boost, salience_boost, recency_boost,
    exact_match_boost, graph_adjacency_boost, graph_cross_source_boost,
    session_demote_factor, reranker_delta
All optional; T4-T6 populate them.

Test coverage: 7/7 hermetic PGLite cases. Empty input, singleton,
same-source hub, cross-source attribution including the
"linked-only-from-other-source" case (widget in source b, linked
from alice+bob in source a → cross_source_hits=1), JSDoc HAVING>=1
contract. Postgres parity asserted by SQL-shape identity (will get a
mirror Postgres E2E in T10's eval gate work via DATABASE_URL when
set; PGLite hermetic case shipped now).

NULL source_id COALESCE branch noted as untestable in current PGLite
schema (pages.source_id is NOT NULL); kept as defense-in-depth.

Plan ref: T3 in v0.40.4.0 wave plan; D1=A, D3=A, D15=A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T4+T11: applyGraphSignals 4th stage in runPostFusionStages

New file src/core/search/graph-signals.ts. Three signals:

  1. Adjacency-within-top-K (×1.05): hits >= 2 inbound from in-set.
  2. Cross-source adjacency (×1.10, stacks): cross_source_hits >= 2.
     Dormant on single-source brains.
  3. Session diversification (×0.95): if multiple top-K share a slug
     prefix, keep highest scoring, DEMOTE the rest. NOT amplify —
     codex caught the original framing was backwards (amplification
     of redundancy makes the cited "weak chunks compete for budget"
     problem worse, not better).

Conservative magnitudes (D14=B): 1.05/1.10/0.95. Score-distribution
probe (onScoreDistribution) collects min/p25/p50/p75/p95/max +
reorder_band_width to feed T-todo-2 magnitude calibration wave.

Slot: 4th stage inside runPostFusionStages (hybrid.ts:248), AFTER
backlink/salience/recency, pre-dedup. Inherits the v0.35.6.0
floor-ratio gate from computeFloorThreshold — this is the structural
protection that prevents a low-cosine hub from outranking a strong
non-hub (codex T2 / D1=A).

PostFusionOpts extends with graphSignalsEnabled, onGraphMeta,
onScoreDistribution. Caller (hybridSearch in subsequent T5 work)
resolves graph_signals from the mode bundle.

Source-scope contract preserved: getAdjacencyBoosts takes raw
page_ids, no source filter. Adjacency is in-set restricted so
cross-source leakage is impossible by construction (D3=A).

Fail-open: engine throw → JSONL audit row via shared createAuditWriter
(T1/T2 primitive, featureName='graph-signals-failures') + meta.errored
+ caller's results unchanged. Session diversification ALSO skips on
failure (predictable all-or-nothing posture).

Mutation note (codex #9): score mutated in place. base_score must be
stamped at runPostFusionStages entry BEFORE this stage so eval-capture
sees pre-boost score (T6 attribution wave).

Test coverage (24 cases, including T11 IRON RULE regression):
  - sessionPrefix multi/single/empty cases
  - computeScoreDistribution percentile math
  - Disabled + empty short-circuits
  - Adjacency hit, no-hit, cross-source stacking, cross-source alone
  - Session diversification 3-share + single-segment + singleton
  - Test seam injection (no engine call)
  - Fail-open: throw → audit row + meta.errored + unchanged
  - Empty Map → session still runs
  - Score-distribution always emits when enabled
  - Meta carries fire counts + duration_ms
  - Missing page_id silently skipped from dedup set
  - **T11 IRON RULE regression (3 cases):**
    * weak hub BELOW floor_threshold does NOT get boosted past
      above-floor non-hub (the bug class the floor gate exists for)
    * hub AT floor still gets boosted (gate is < not <=)
    * NaN score → NaN >= threshold is false → no boost

Plan ref: T4 + T11 in v0.40.4.0 wave plan; D1=A, D2=A, D11=B, D14=B,
D9=A, D5=B. Codex outside-voice #1 + #2 + #6 + #8 + #9 addressed.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T5: graph_signals mode-bundle knob + KNOBS_HASH bump 3→4

ModeBundle gains graph_signals: boolean. Per-mode defaults:
  - conservative: false (cost-sensitive tier)
  - balanced:     true (the wave's primary surface for default-on)
  - tokenmax:     true (power-user tier, capstone fit)

SearchKeyOverrides + SearchPerCallOpts gain optional graph_signals
field. resolveSearchMode picks via the standard per-call → config
override → mode bundle chain.

loadOverridesFromConfig parses 'search.graph_signals' from the config
table ('1' or 'true' → true). SEARCH_MODE_CONFIG_KEYS adds the key
so `gbrain search modes --reset` clears it alongside other knobs.

KNOBS_HASH_VERSION bump 3→4 (append-only per CDX2-F13). New `gs=`
parts entry appended AFTER cross-modal + column + prov entries. A
graph-on cache write cannot be served to a graph-off lookup —
mid-deploy hit-rate dip clears within cache.ttl_seconds (3600s).

src/commands/search.ts KNOB_DESCRIPTIONS gains graph_signals entry
so `gbrain search modes` dashboard renders the new knob.

Test coverage:
  - test/search-mode.test.ts (+ 8 new cases): per-mode defaults
    canonical, config override both directions, per-call override
    wins, knobsHash distinct for on/off, config key registered,
    attributeKnob reports per-call + mode sources correctly.
  - test/search/knobs-hash-reranker.test.ts: version assertion
    bumped 3→4 with v0.40.4 rationale comment.
  - test/cross-modal-phase1.test.ts: version assertion bumped
    3→4 with v0.40.4 rationale comment.
  - Canonical-bundle assertions updated to include graph_signals
    in expected shape (3 cases).

50/50 search-mode tests pass. 45/45 cross-modal pass. 17/17
knobs-hash-reranker pass. 10/10 balanced-reranker pass.

Plan ref: T5 in v0.40.4.0 wave plan.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T6: per-stage attribution stamping in every boost

Every boost stage that mutates SearchResult.score now stamps a field
recording WHAT it multiplied:

  - applyBacklinkBoost  → backlink_boost (skipped when count == 0)
  - applySalienceBoost  → salience_boost (skipped when score == 0)
  - applyRecencyBoost   → recency_boost (skipped on evergreen prefix)
  - applyExactMatchBoost → exact_match_boost (skipped on no-match
    OR when intent's exactMatchBoost == 1.0 no-op)
  - runPostFusionStages → base_score stamped ONCE at entry, BEFORE
    any boost mutates r.score. Idempotent: caller-pre-stamped value
    preserved. Empty-results short-circuit unchanged.
  - applyReranker → reranker_delta = original_index - new_index
    (positive = rank improved; raw rerank score stays in rerank_score)
  - applyGraphSignals → graph_adjacency_boost, graph_cross_source_boost,
    session_demote_factor (T4 already stamped these)

Why: feeds the T7 `gbrain search --explain` formatter so it can
attribute the final score to its components. Without these stamps,
"why did this rank where it did?" is grep-and-guess.

SearchResult.reranker_delta doc updated to clarify it's a RANK delta
(positive = improved), not a score delta. The raw relevance score
stays in `rerank_score` (untyped, for back-compat with telemetry that
already reads it).

Test coverage: 16 new cases in test/search/attribution-stamping.test.ts.
Pins: every boost stamps when it fires AND skips stamping when it
doesn't (no false attribution on no-op stages). base_score idempotency
preserved. reranker_delta computed correctly across rank-improved +
rank-degraded cases.

All 178/178 search tests pass (no regressions).

Plan ref: T6 cathedral expansion in v0.40.4.0 wave plan; D12=A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T7: gbrain search --explain per-stage attribution

New file src/core/search/explain-formatter.ts renders SearchResult[]
as a multi-line breakdown of how the final score was formed:

  1. people/alice (score=12.4)
     base=10.2 (rrf+cosine)
     + backlink ×1.08
     + salience ×1.05
     + adjacency ×1.05 (hits=3)
     + cross_source ×1.10 (other_sources=2)
     ↑ reranker rank +2
     = final 12.4

Reads the boost_* / base_score / *_hits fields populated by T4 + T6.
Empty path: "no boosts applied" when no stage stamped anything.
Session demote rendered with `-` prefix (not `+`) so the demotion
direction is visually distinct from boosts.

CliOptions gains `explain: boolean`; parseGlobalFlags recognizes
`--explain` anywhere in argv. cli.ts formatResult for `search` +
`query` cases reads CliOptions.explain via the module-level
singleton and routes to formatResultsExplain when set. Lazy import
keeps the hot path narrow for the common non-explain case.

Number formatting: 4-decimal precision, trailing zeros stripped
('1.0000' → '1', '0.1234' → '0.1234'). NaN preserved as 'NaN'.

Test coverage:
  - test/search/explain-formatter.test.ts: 19 cases pin output
    format. Each boost type renders correctly, every-stage stacking
    composes, reranker_delta=0 doesn't render, empty list short-
    circuits, rank numbering 1-based, number formatting edge cases.
  - test/cli-options.test.ts: 3 new cases for --explain parsing
    (basic, absent default, any-argv-position).

Existing CliOptions literals in test/cli-options.test.ts +
test/thin-client-upgrade-prompt.test.ts updated for new required
explain field.

JSON envelope unchanged — the same attribution fields surface in
existing --json output via JSON.stringify; no separate JSON formatter
needed.

Plan ref: T7 cathedral expansion in v0.40.4.0 wave plan; D12=A + D6=A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T8: doctor check graph_signals_coverage

New checkGraphSignalsCoverage in src/commands/doctor.ts. Wired into
both runDoctor (local engine) and doctorReportRemote (HTTP MCP /
JSON path) so local AND remote-server brains both surface the metric.

Logic:
  1. Resolve active graph_signals setting: config override
     'search.graph_signals' wins, else mode bundle default
     ('search.mode' → conservative=false, balanced/tokenmax=true).
  2. When disabled → silent ok ("disabled — coverage not checked").
     Avoids polluting doctor output on installs that don't use the
     feature.
  3. When enabled, compute global inbound-link density:
     COUNT(DISTINCT to_page_id) / COUNT(*) across non-deleted pages.
  4. <10% → warn ("signal will rarely fire") with paste-ready
     `gbrain extract all` fix hint.
  5. >=30% → ok ("fire on most queries") with metric.
  6. 10-29% → ok ("fire occasionally") with metric.

Known limitation (codex outside-voice #14): global density is an
imperfect proxy for "top-K subgraphs have enough edges to fire."
T-todo-5 captures the v0.41+ refinement that measures actual fire
rate from search-stats after 30 days of data.

Best-effort: SQL errors → warn with the underlying message. Never
breaks doctor.

Test coverage (7 new cases in test/doctor.test.ts):
  - conservative mode → silent ok regardless of coverage
  - balanced default + 0 links → warn at 0% with fix hint
  - balanced default + 40% inbound → ok "fire on most queries"
  - balanced default + 20% inbound → ok "fire occasionally"
  - explicit search.graph_signals=false overrides mode default
  - empty brain → ok with explanation
  - check is wired into runDoctor (source-grep regression guard)

All 55/55 doctor.test.ts cases pass.

Plan ref: T8 in v0.40.4.0 wave plan; D6=A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T9: gbrain search stats graph_signals section

runStatsSubcommand in src/commands/search.ts gains a graph_signals
section in both --json and human output:

  Graph signals:
    enabled:    true (mode default)
    failures:   3 fail-open event(s)
      ECONNREFUSED         2
      timeout              1

Data sources:
  - config: 'search.graph_signals' override → enabled + source=config,
    otherwise mode-bundle default → enabled + source=mode_default.
  - JSONL audit: readRecentGraphSignalsFailures(days) returns events;
    failures_count is len, failures_by_reason buckets by first word of
    error_summary (e.g. 'ECONNREFUSED', 'timeout').

JSON envelope (schema_version 2 unchanged; graph_signals is a new
sibling property of stats, so consumers reading the existing fields
keep working):

  {
    "schema_version": 2,
    ...stats...,
    "graph_signals": {
      "enabled": bool,
      "source": "config" | "mode_default",
      "failures_count": int,
      "failures_by_reason": { reason: count }
    },
    "_meta": { metric_glossary: { ..., graph_signals_enabled: ..., graph_signals_failures_count: ... } }
  }

Fire-rate metrics (adjacency_fires, cross_source_fires,
session_demotions) and score-distribution stats are NOT in this
section yet — they require telemetry-table writes from the
applyGraphSignals onMeta callback. Wired in v0.41+ via T-todo-2
calibration wave (the wave that needs them). For v0.40.4: status +
error count is the actionable surface for "is graph_signals on, and
is it failing?"

Human output: prints the section after the existing stats block.
Edge case: when total_calls is 0 BUT graph_signals is enabled OR
has historical failures, still prints the section so operators
don't lose the signal on a brain with no telemetry yet.

Test coverage (6 cases in test/search/search-stats-graph-signals.test.ts):
  - search.graph_signals=true → enabled true, source=config
  - mode=conservative → enabled false, source=mode_default
  - no config → enabled true (balanced default), source=mode_default
  - JSONL failures bucketed by first word of error_summary
  - empty audit → failures_count 0, empty failures_by_reason
  - human output includes "Graph signals:" header

Plan ref: T9 in v0.40.4.0 wave plan; D6=A.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T10: eval gates (longmemeval-mini A/B + paired bootstrap)

New test/e2e/graph-signals-eval.test.ts runs each longmemeval-mini
question twice (graph_signals off, graph_signals on) and asserts:

  Gate 1 (QUALITY) — paired bootstrap, 10,000 resamples:
    - If signals-on is significantly WORSE than off
      (delta < 0 AND p < 0.05) → fail.
    - Otherwise pass. p>=0.05 either direction OR delta >= 0 → ok.

  Gate 2a (CHANGE-MAGNITUDE): mean Jaccard@5 over result-set overlap
    must be >= 0.5. If results overlap less than half, the change is
    too large and needs human review before default-on.

  Gate 2b (CHANGE-MAGNITUDE): top-1 stability rate >= 0.7. If 30%+
    of top picks change, hard look required.

  Gate 3 (HARD ABSOLUTE FLOOR): recall@5 drop <= 5pt. Catastrophic
    regression catch (codex outside-voice #18 — addresses the "top-5
    must not drop at all" brittleness on tiny fixtures).

Bootstrap implementation:
  - Per-question observation is binary (recall@5 hit/miss).
  - Paired pairing on question_id between on/off branches.
  - Centered distribution under null (subtract observed mean) per
    standard paired-bootstrap-shift approach for binary outcomes.
  - Two-tailed p-value: |resampled delta| >= |observed delta|.
  - Deterministic seeded RNG so test runs are stable across CI.

pairedBootstrapPValue exported as a pure function with separate
tests for edge cases (empty input, all-equal, strong positive, strong
negative, determinism). Reusable from future calibration waves.

Hermetic: in-memory PGLite via createBenchmarkBrain + resetTables
between questions. No API keys needed (--no-embed import path
exercises keyword-only retrieval). Skips gracefully via describe.skip
when the fixture is missing.

Plan ref: T10 in v0.40.4.0 wave plan; D7=C absolute floor + D13=A
paired bootstrap; codex #4 + #18 stability-vs-quality distinction.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 T12: VERSION + package.json + CHANGELOG + TODOS

VERSION: 0.37.11.0 → 0.40.4.0
package.json: 0.37.11.0 → 0.40.4.0
CHANGELOG.md: top entry for v0.40.4.0 in ELI10-lead voice per
  CLAUDE.md release rules. Lead is plain-English ("Your search now
  notices when a page is a hub for your query"); precise file paths
  / SQL semantics / numbers live in the "Itemized changes" section
  below. Includes the cathedral-expansion notes (D5=B audit
  unification, D12=A per-stage attribution, D13=A eval gates) and
  the "To take advantage of v0.40.4.0" verify-and-fix block.

TODOS.md: 5 new items captured under "v0.40.4 graph signals —
deferred follow-ups (v0.41+)":
  - T-todo-1: profile graph-signal SQL latency, merge if hot (D8=C)
  - T-todo-2: magnitude calibration wave from probe data (D14=B / D17)
  - T-todo-3: DB-backed audit table for cross-deploy observability (codex #15)
  - T-todo-4: sync-topology-aware cross-source signal (codex #11)
  - T-todo-5: replace doctor's global density with fire-rate (codex #14)

Verified the 3-line audit: VERSION + package.json + CHANGELOG topmost
all match 0.40.4.0. `bun install` ran (lockfile unchanged — root
package version isn't stored in bun.lock). `bun run build:llms`
refreshed llms.txt + llms-full.txt for the next commit.

Plan ref: T12 in v0.40.4.0 wave plan.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 TODO: document pre-existing shard-2 flake noticed during ship

3 isCacheSafe test failures in shard 2 reproduce on stashed clean
master. Confirmed pre-existing — not introduced by v0.40.4. Filed
under "Pre-existing flake on master (noticed during v0.40.4 ship)"
with reproduction commands + remediation options. Shipping v0.40.4
through it; future wave can fix.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 privacy scrub: replace wintermute → media in example slugs

CLAUDE.md line 550 bans the private OpenClaw fork name in public
artifacts. Example session prefix in sessionPrefix() docs + 3 test
fixtures swept to 'media/chat/...' instead. Pre-existing
scripts/check-privacy.sh in `bun run verify` caught it.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 fix: wire graph_signals from mode bundle to runPostFusionStages

CRITICAL: pre-landing review (codex outside-voice via /ship Step 9)
caught that hybrid.ts's `postFusionOpts` literal at line 566 was
building PostFusionOpts WITHOUT threading `resolvedMode.graph_signals`
to `graphSignalsEnabled`. The gate at hybrid.ts:358 read the field
from a literal that never set it.

Result before this fix: the entire v0.40.4 graph-signals wave was
dead code in production. Mode bundles set
`balanced.graph_signals = true` and `tokenmax.graph_signals = true`,
but no production call site ever reached applyGraphSignals. The
KNOBS_HASH bump 3→4 correctly varied the cache key by the flag, so
contamination was prevented — but the feature itself never fired.

All shipped infrastructure (engine SQL, fail-open audit, attribution
stamps, --explain formatter, doctor coverage check, search-stats
section) was reachable only through the unit-test seam
(`opts.adjacencyFn`). The CHANGELOG-advertised behavior never
landed in user-visible search.

Fix: thread `graphSignalsEnabled: resolvedMode.graph_signals` into
the postFusionOpts literal (1 line). Inline comment names codex's
catch so future refactors see the regression class.

Tests: new test/search/graph-signals-wire-integration.test.ts pins
the wire end-to-end. Three cases:
  1. balanced mode → hybridSearch on a seeded brain with adjacency
     hub produces a result with base_score stamped (proves
     runPostFusionStages actually ran).
  2. search.graph_signals=false config override → no graph_* fields
     stamped (proves the gate honors the override path).
  3. Source-grep regression guard pinning the
     `graphSignalsEnabled: resolvedMode.graph_signals` literal in
     hybrid.ts so a future refactor can't silently disconnect.

All 57 existing v0.40.4 wave tests still pass. Typecheck clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 fix: pre-landing review AUTO-FIX findings (audit msg drift + deleted_at)

Two informational findings from /ship pre-landing review (Step 9):

1. Stderr message qualifier drift (rerank/slug-fallback/phantom audits)
   Pre-v0.40.4 messages included a per-feature qualifier:
     [gbrain] rerank-failure audit write failed (...)
     [gbrain] slug-fallback audit write failed (...)
     [gbrain] phantom audit write failed (...)
   The T2 refactor dropped the qualifier (plan promised "byte-identical"
   operator-visible behavior, but stderr lines did drift). Restored via
   new `errorMessagePrefix` option on `createAuditWriter` (optional, ''
   default). Three modules pass the per-feature qualifier; shell-audit
   and supervisor-audit unaffected (their pre-v0.40.4 messages didn't
   have a separate qualifier — label already carried the feature name).

2. Defense-in-depth `deleted_at IS NULL` on getAdjacencyBoosts
   SQL was previously protected by-construction (hybridSearch's
   visibility filter ensures input pageIds are live), but matches the
   v0.35.5.0 findOrphanPages pattern and closes the bug class if a
   future caller bypasses hybridSearch. Added to both Postgres and
   PGLite engines for parity. Three JOIN sites guarded (targets CTE,
   FROM-pages join). One inline comment per engine cites the codex
   review and the v0.35.5.0 precedent.

Plan ref: /ship pre-landing review v0.40.4.0 (codex finding C and F).

All 84 audit+graph-signals tests pass. Typecheck clean.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 fix: adversarial review HIGH findings (codex H1+H2 + Claude F1)

Three HIGH-severity issues from /ship adversarial pass:

H1 (Codex): Eval gate was a no-op.
  Test passed `graph_signals: graphSignalsOn` via `as any` cast, but
  SearchOpts had no field and hybridSearch's perCall didn't thread it.
  Both off/on branches resolved to the mode-bundle default — gate
  measured identical behavior, could pass while detecting nothing.

  Fix: add `graph_signals?: boolean` to SearchOpts (types.ts:794).
  Thread `opts.graph_signals` into perCall in both hybridSearch
  (hybrid.ts:425) AND hybridSearchCached (hybrid.ts:1027) so the
  cache-key resolver also sees the override. Drop the `as any` from
  the eval test — types are real now.

H2 (Codex): Session diversification fired on entity directories.
  sessionPrefix() used "any shared parent directory" as the session
  signal. Result: a search for "people in SF" returned `people/alice`
  + `people/bob` + `people/charlie` and the latter two got demoted
  to 0.95×. Every common entity-search query silently penalized
  legitimate same-type results. Default-on for balanced/tokenmax
  means production behavior was wrong.

  Fix: narrow sessionPrefix() to fire ONLY when the slug contains a
  session-like marker (`chat`/`session`/`sessions` segment OR a
  `YYYY-MM-DD` date segment). Entity directories (`people/`,
  `companies/`, `docs/`) return null → diversification skips.
  Returns NULL (not the slug itself) so the loop skips clean.
  Examples in JSDoc:
    your-agent/chat/2026-05-20-foo → 'your-agent/chat/2026-05-20-foo'
    daily/2026-05-20/journal-entry-1 → 'daily/2026-05-20'
    transcripts/chat/funding-discussion → 'transcripts/chat/funding-discussion'
    people/alice → null  ← codex H2 regression
    docs/quickstart → null

F1 (Claude adversarial subagent): case-sensitivity drift across 3 sites.
  loadOverridesFromConfig in mode.ts is case-insensitive +
  whitespace-trimmed for 'search.graph_signals' values. But
  doctor's checkGraphSignalsCoverage (doctor.ts:899) AND
  search-stats's readGraphSignalsStats (search.ts:288) used
  case-sensitive compare. User sets `search.graph_signals TRUE`:
  production enables the feature, but doctor + search-stats both
  silently report disabled. Operators lose the only observability
  surface for the new feature on values like 'True'/'TRUE'.

  Fix: trim + lowercase parity at both sites. Mirror the parser's
  semantic. Also case-normalized `search.mode` reads at both sites
  for the same divergence class.

Tests:
  - sessionPrefix block rewritten with 7 cases covering chat marker
    + date anchor + entity dirs (now-NULL) + degenerate (no /).
  - Added regression test pinning codex H2: people/alice +
    people/bob + people/charlie do NOT get diversified.
  - graph-signals-eval.test.ts drops `as any` — typed field works.
  - Existing tests using `chat/a`/`chat/b` updated to session-shaped
    `media/2026-05-20/chunk-a` so the date anchor actually fires.

111/111 graph-signals + doctor + search-stats tests pass. Typecheck clean.

Plan ref: /ship adversarial review v0.40.4.0 (codex H1, H2; Claude F1).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* v0.40.4.0 TODOs: capture 11 LOW adversarial findings for v0.41+

Codex L1 (audit window underreport) + Claude F2/F3/F5-F8/F11/F12/F14/F16
from /ship adversarial review. None are load-bearing; all captured under
'v0.40.4 adversarial review LOW findings — captured for v0.41+'.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs: update project documentation for v0.40.4.0

- README: surface v0.40.4.0 graph signals + --explain in Hybrid search capability
- CLAUDE.md: annotate engine.ts getAdjacencyBoosts, new graph-signals.ts /
  explain-formatter.ts / audit/audit-writer.ts, plus hybrid.ts post-fusion
  4th stage, mode.ts graph_signals knob + KNOBS_HASH 3→4, cli-options.ts
  --explain flag, search stats + doctor coverage check
- llms-full.txt: regenerated from CLAUDE.md per the build:llms chaser rule

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix(ci): pin bun-version to 1.3.13 across all workflows

setup-bun action with `bun-version: latest` calls the GitHub API
(https://api.github.com/repos/oven-sh/bun/git/refs/tags) to resolve
the tag. CI started failing today with HTTP 401 "Bad credentials"
even though the action receives a token (visible as `token: ***`
in the run log). Pinning the version eliminates the API call
entirely.

Affected workflows: test.yml, e2e.yml, release.yml, heavy-tests.yml
(5 invocations total). Pinned to 1.3.13 — matches package.json
engines (`bun >= 1.3.10`) and the version v0.40.4.0 was developed
against.

Bump cadence: when a new bun version is required, update this
pin in one PR. Trading "always-latest" for "always-deterministic"
is the right trade for a 5-shard CI matrix.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-05-23 10:01:08 -07:00
Garry TanandClaude Opus 4.6 eb218a96ad security: pin GitHub Actions, add gitleaks CI, harden permissions (v0.4.2) (#23) 
* security: pin GitHub Actions to commit SHAs, add gitleaks CI

- Pin all 5 actions (checkout, setup-bun, upload-artifact, download-artifact,
  action-gh-release) to commit SHAs across 3 workflow files
- Add permissions: contents: read to test.yml and e2e.yml
- Add gitleaks secret scanning job to test.yml
- Pin openclaw install to v2026.4.9 in e2e.yml

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

* security: add .gitleaks.toml config

Allowlists test fixtures, example env files, and skill documentation
to prevent false positives from the gitleaks CI step.

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

* docs: add GitHub Actions SHA maintenance rule to CLAUDE.md

Instructs /ship and /review to check for stale SHA pins and update
them, keeping action versions fresh without manual effort.

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

* docs: add S3 Sig V4 TODO from CSO audit

Deferred from security audit. S3 storage backend accepts credentials
but sends unsigned requests. Implement when S3 becomes a real
deployment path.

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

* chore: bump version and changelog (v0.4.2)

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 05:26:09 -10:00
Garry TanandClaude Opus 4.6 a86f995883 feat: GBrain v0.3.0 — contract-first architecture + ClawHub plugin (#7) 
* feat: contract-first operations.ts with OperationError, dry_run, importFromContent

30 shared operations as single source of truth for CLI and MCP.
- OperationError with typed error codes (page_not_found, invalid_params, etc.)
- dry_run support on all mutating operations
- importFromContent split from importFile with transaction wrapping
- Idempotency hash now includes ALL fields (title, type, frontmatter, tags)
- Config env var fallback: GBRAIN_DATABASE_URL > DATABASE_URL > config file

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

* refactor: rewrite MCP server + CLI + tools-json from operations

server.ts: 233 -> ~80 lines. Tool definitions and dispatch generated from operations[].
cli.ts: shared operations auto-registered, CLI-only commands kept as manual dispatch.
tools-json: generated FROM operations[], eliminating the third contract surface.
Parity test verifies structural contract between operations, CLI, and MCP.

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

* refactor: delete 12 command files migrated to operations.ts

Handler logic for get, put, delete, list, search, query, health, stats,
tags, link, timeline, and version now lives in operations.ts.
Kept: init, upgrade, import, export, files, embed, sync, serve, call, config.

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

* feat: init --non-interactive, upgrade verification, schema migration

- gbrain init --non-interactive --url <url> for plugin mode (no TTY required)
- Post-upgrade version verification in gbrain upgrade
- Drop storage_url from files table (storage_path is the only identifier)

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

* feat: tool-agnostic skills + new setup skill

All 7 skills rewritten with intent-based language instead of CLI commands.
Works with both CLI and MCP plugin contexts.
New setup skill replaces install: auto-provision Supabase via CLI,
AGENTS.md injection, target TTHW < 2 min.

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

* feat: ClawHub bundle plugin, CI workflows, v0.3.0

- openclaw.plugin.json with configSchema, MCP server config, skill listing
- GitHub Actions: test on push/PR, multi-platform release (macOS arm64 + Linux x64)
- Version bump 0.3.0, CHANGELOG, README ClawHub section, CLAUDE.md updated

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

* fix: idempotency hash mismatch + MCP dry_run passthrough

importFromContent now passes its all-fields hash through putPage via
content_hash on PageInput, so the stored hash matches the computed hash.
Previously the skip-if-unchanged check never fired because the hash
formulas differed.

MCP server now passes dry_run from tool params to OperationContext.

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

* chore: bump version and changelog (v0.3.0.0)

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

* fix: schema loader handles PL/pgSQL $$ blocks

Delete the semicolon-based SQL splitter in db.ts which broke on
PL/pgSQL trigger functions containing semicolons inside $$ delimiter
blocks. Use single conn.unsafe(schemaSql) call instead — the postgres
driver handles multi-statement SQL natively. schema.sql already uses
IF NOT EXISTS / CREATE OR REPLACE for idempotency.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* feat: E2E test infrastructure + realistic brain fixtures

Add test infrastructure for running E2E tests against real
Postgres+pgvector. Includes:
- test/e2e/helpers.ts: DB lifecycle, fixture import, timing, diagnostics
- 13 fixture files as a miniature realistic brain (people, companies,
  deals, meetings, concepts, projects, sources) following the
  compiled truth + timeline format from GBRAIN_RECOMMENDED_SCHEMA.md
- docker-compose.test.yml: local pgvector convenience (port 5433)
- .env.testing.example: template for test credentials
- package.json: add test:e2e script

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* feat: E2E test suites + CI workflow

Tier 1 (mechanical.test.ts): 14 test suites covering all operations
against real Postgres — page CRUD, search with quality scoring, links,
tags, timeline, versions, admin, chunks, resolution, ingest log, raw
data, files, idempotency stress, setup journey (full CLI flow), init
edge cases, schema idempotency, schema diff guard, performance baselines.

Tier 1 (mcp.test.ts): MCP protocol test — spawns server, sends JSON-RPC,
verifies tools/list matches operations count.

Tier 2 (skills.test.ts): OpenClaw skill tests — ingest, query, health.
Skips gracefully when dependencies missing.

CI (.github/workflows/e2e.yml): Tier 1 on every PR (pgvector service),
Tier 2 nightly/manual with API key secrets.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: E2E test fixes + traverseGraph jsonb cast

- Fix traverseGraph query: cast json_agg to jsonb_agg so SELECT DISTINCT works
- Fix put_page tests to use importFromContent with noEmbed (no OpenAI key in Tier 1)
- Fix get_health assertion (page_count not total_pages)
- Fix raw_data test to handle JSONB string/object return
- Simplify MCP test to verify tool generation directly
- Add timeouts to CLI subprocess tests
- Use port 5434 for docker-compose (5433 often in use)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* docs: update all project docs for E2E test suite

- CLAUDE.md: updated test count (9 unit + 3 E2E), added E2E test
  instructions, fixed skill count to 8
- CONTRIBUTING.md: updated project structure with test/e2e/, added E2E
  test instructions, rewrote "Adding a new command" to reflect
  contract-first architecture (add to operations.ts, done)
- README.md: fixed table count (10 not 9), added recommended schema doc
  to Docs section, added E2E instructions to Contributing section
- CHANGELOG.md: added E2E test suite, docker-compose, schema loader fix,
  and traverseGraph jsonb fix to v0.3.0 entry

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 2026-04-08 23:26:11 -10:00