fix: zombie PID lock detection + self-healing jsonb repair in dream cycle by garrytan · Pull Request #539 · garrytan/gbrain

garrytan · 2026-04-30T18:31:35Z

Problem

The dream cycle's synthesize and patterns phases (v0.23.0) successfully ran subagent jobs that wrote brain pages via brain_put_page tool calls — but the orchestrator consistently reported 0 pages written. All synthesized content was silently lost: never reverse-written to disk, never committed to git, never surfaced in the cycle summary.

Additionally, zombie (defunct) bun processes were holding Postgres cycle locks indefinitely, blocking subsequent cycle runs even though the holder process was dead.

Production impact

A 54K-page production brain ran its first synthesize cycle: 8 subagents completed successfully, each writing 2 pages (16 total). The cycle summary reported pages_written: 0.
The patterns phase then ran: 1 subagent wrote 3 pattern pages. Summary: patterns_written: 0.
19 brain pages existed only in Supabase with no disk/git representation.
Zombie bun workers held cycle locks for 30+ minutes, causing cycle_already_running blocks on every dream attempt.

Error Log

Synthesize cycle summary (production):

{
  "phases": [{
    "phase": "synthesize",
    "status": "ok",
    "summary": "8 transcript(s) synthesized in 398.2s",
    "details": {
      "transcripts_discovered": 90,
      "transcripts_processed": 8,
      "pages_written": 0,
      "reverse_write_count": 0,
      "child_outcomes": [
        {"jobId": 2653, "status": "completed"},
        {"jobId": 2654, "status": "completed"},
        {"jobId": 2655, "status": "completed"},
        {"jobId": 2656, "status": "completed"},
        {"jobId": 2657, "status": "completed"},
        {"jobId": 2658, "status": "completed"},
        {"jobId": 2659, "status": "completed"},
        {"jobId": 2660, "status": "completed"}
      ]
    }
  }]
}

Diagnostic query showing the root cause — input column stored as jsonb string instead of jsonb object:

SELECT id, jsonb_typeof(input) as input_type, input->>'slug' as slug
FROM subagent_tool_executions
WHERE tool_name = 'brain_put_page' AND status = 'complete';

-- id  | input_type | slug
-- 502 | string     | NULL   ← can't extract keys from a string
-- 504 | string     | NULL
-- ...all 16 successful writes return NULL

Zombie lock holder blocking cycle runs:

$ ps -p 1619018 -o pid,stat,cmd
PID  STAT CMD
1619018 Z  [bun] <defunct>

$ SELECT * FROM gbrain_cycle_locks;
-- id: gbrain-cycle, holder_pid: 1619018, ttl_expires_at: +30min
-- PID 1619018 is a zombie — passes kill(pid,0) but can never release the lock

What We Tried

Ran gbrain dream --phase synthesize — returned cycle_already_running (zombie lock).
Manually cleared zombie lock rows in gbrain_cycle_locks — synthesize then ran but hit 12h cooldown (it had already run once, producing the 0-pages-written result).
Queried subagent_tool_executions directly — found all 16 brain_put_page calls with status: 'complete' and full content in the input column.
Diagnosed the encoding: jsonb_typeof(input) returned 'string' instead of 'object'. The input ? 'slug' operator (jsonb key-existence) fails on string values, so collectChildPutPageSlugs returned 0 rows.
Traced to root cause: persistToolExecPending() called JSON.stringify(input) before passing to executeRaw() with ::jsonb cast. The postgres library's .unsafe() method sends string parameters as text — Postgres receives '{"slug":"..."}' as a text string and casts it to a jsonb string scalar (wrapped in quotes), not a jsonb object.
Verified with test: passing a raw object to .unsafe() with ::jsonb correctly stores a jsonb object; JSON.stringify() + ::jsonb produces a double-encoded jsonb string.

Solution

Fix 1: Remove JSON.stringify() from persist functions (already on master, `80b3909`)

src/core/minions/handlers/subagent.ts — all three persist functions:

// Before (wrong):
[jobId, messageIdx, toolUseId, toolName, JSON.stringify(input)]

// After (correct):
const jsonbInput = (input != null && typeof input === 'object')
  ? input
  : { _raw: String(input ?? '') };
[jobId, messageIdx, toolUseId, toolName, jsonbInput]

The postgres driver's .unsafe() correctly serialises objects to jsonb objects. JSON.stringify() adds a layer of string escaping that produces a jsonb string scalar.

Fix 2: Self-healing jsonb repair in collectChildPutPageSlugs (this PR)

src/core/cycle/synthesize.ts and src/core/cycle/patterns.ts:

Before querying for slugs, run an idempotent fixup:

UPDATE subagent_tool_executions
   SET input = (input #>> '{}')::jsonb
 WHERE job_id = ANY($1::int[])
   AND jsonb_typeof(input) = 'string'
   AND (input #>> '{}') IS NOT NULL
   AND left(input #>> '{}', 1) = '{'

input #>> '{}' extracts the text content of a jsonb string, then ::jsonb re-parses it as a proper jsonb object. Only touches rows where the encoding is wrong. Ensures older runs' data is accessible without a separate migration.

Fix 3: Zombie PID detection in cycle lock acquisition (this PR)

src/core/cycle.ts:

New isZombiePid(pid) reads /proc/<pid>/status and checks for State: Z:

function isZombiePid(pid: number): boolean {
  try {
    const status = readFileSync(`/proc/${pid}/status`, 'utf-8');
    return /^State:\s+Z/m.test(status);
  } catch { return false; }
}

Postgres lock path (acquirePostgresLock): When the TTL-based upsert returns empty (lock held), check if the holder PID on the same host is a zombie. If so, delete the lock row and retry acquisition.

File lock path (acquireFileLock): The existing pidAlive check now uses !isZombiePid(existingPid) — zombies are treated as dead.

Behavior matrix

Scenario	Before	After
Subagent writes page via `brain_put_page`	Stored as jsonb string; orchestrator can't find it	Stored as jsonb object; orchestrator finds it
Older double-encoded rows in DB	Silent 0-page results forever	Auto-repaired on next cycle run
Zombie bun process holds cycle lock	Blocks all cycles for 30 min until TTL expires	Detected via /proc, lock cleared, cycle proceeds
Non-zombie process holds lock (normal)	Correctly waits/skips	Unchanged — no false positives
macOS/non-Linux (no /proc)	N/A	`isZombiePid` returns false, falls back to existing TTL behavior

Results

After deploying fix 1 (80b3909) and manually repairing the data:

16 synthesized pages recovered from DB and committed to git (8 reflections + 8 originals/ideas)
3 pattern pages recovered (cross-session themes)
New worker (restarted with fix 1) correctly stores jsonb objects
Fix 2 (this PR) ensures any remaining pre-fix rows are auto-repaired
Fix 3 (this PR) eliminates the zombie lock blocking pattern

Testing

bun run typecheck passes
Verified JSON.stringify(obj) + ::jsonb produces jsonb string via production test
Verified raw object + ::jsonb produces jsonb object via production test
Verified isZombiePid() correctly identifies defunct processes in production
Verified self-healing fixup query on 53 double-encoded rows in production
Manual end-to-end: synthesize → subagent writes → orchestrator collects slugs → reverse-write to disk → git commit

…ycle Three fixes for production dream cycle reliability: 1. Zombie PID detection in cycle lock acquisition (cycle.ts): - kill(pid, 0) returns success for zombie (defunct) processes - Zombies can never release the lock or refresh TTL - New isZombiePid() reads /proc/<pid>/status for State: Z - acquirePostgresLock() clears zombie holders on same host - acquireFileLock() treats zombie holders as dead 2. Self-healing jsonb repair in collectChildPutPageSlugs (synthesize.ts, patterns.ts): - Pre-fix runs stored input as jsonb string instead of jsonb object - input->>'slug' returned null, so orchestrator reported 0 pages written - New fixup query un-wraps double-encoded rows before the SELECT - Idempotent: only touches rows where jsonb_typeof(input) = 'string' 3. Root cause fix (already on master via 80b3909): - Removed JSON.stringify() from persist functions in subagent.ts - Passes objects directly to postgres driver for correct jsonb encoding

JSON.stringify(input) + ::jsonb cast produced a jsonb string value instead of a jsonb object. The postgres library's unsafe() with a raw object + ::jsonb correctly stores a jsonb object. This caused collectChildPutPageSlugs to return 0 results (can't extract ->>'slug' from a jsonb string), making dream synthesize report '0 pages written' even though subagents successfully wrote 16 pages to the database. Fix: pass objects as-is to executeRaw, let the postgres driver handle serialization. Non-object values wrapped in {_raw: ...} as a safety fallback.

…ter) (#528) * feat: diff-aware E2E test selector Adds scripts/select-e2e.ts: reads git diff vs origin/master, classifies the change set (EMPTY/DOC_ONLY/SRC), and emits the relevant E2E test files on stdout. Fail-closed by design: any unmapped src/ change runs all E2E. - scripts/e2e-test-map.ts: hand-tuned path-glob -> test files map - scripts/select-e2e.ts: pure-function selector with three explicit cases - scripts/run-e2e.sh: accepts optional file list from argv + --dry-run-list - test/select-e2e.test.ts: 24 cases including 3 codex regression guards (skills/, untracked files, unmapped src/) * feat: local CI gate via docker compose Adds bun run ci:local — runs every check GH Actions runs (gitleaks + unit + 29 E2E files) inside a Docker container that bind-mounts the repo. Pure bind-mount + named volumes (gbrain-ci-node-modules, gbrain-ci-bun-cache, gbrain-ci-pg-data) for fast warm restarts. - docker-compose.ci.yml: pgvector/pgvector:pg16 + oven/bun:1 - scripts/ci-local.sh: orchestrator with --diff, --no-pull, --clean - gitleaks runs on host (scoped to working dir + branch commits) - DATABASE_URL unset for unit phase (matches GH Actions split) - git installed in container at startup (oven/bun:1 omits it) - Postgres host port via GBRAIN_CI_PG_PORT env (default 5434) Stronger than PR CI: runs all 29 E2E files vs CI's 2-file Tier 1. * chore: bump version and changelog (v0.23.1) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: document local CI gate for v0.23.1 CLAUDE.md gains key-files entries for docker-compose.ci.yml, scripts/ci-local.sh, scripts/select-e2e.ts + e2e-test-map.ts, and the scripts/run-e2e.sh argv tweak. Pre-ship requirements section now lists the Docker-based local gate as Path A alongside the manual lifecycle. CONTRIBUTING.md tests section adds the bun run ci:local / ci:local:diff / ci:select-e2e block with prerequisites (Docker engine + gitleaks) and the GBRAIN_CI_PG_PORT override. AGENTS.md "Before shipping" promotes ci:local as the easiest path and keeps the manual lifecycle as a fallback. README.md Contributing section points to ci:local for the full gate. CHANGELOG.md untouched — v0.23.1 entry already finalized. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * feat: SHARD=N/M env support in scripts/run-e2e.sh Filters the E2E file list to every M-th file starting at index N (1-indexed). Sequential execution within a shard preserves the TRUNCATE CASCADE no-race property documented at the top of the file. Empty-shard handling under `set -u` uses ${arr[@]:-} fallback. Standalone change; not yet wired up in ci-local.sh. * feat: 4-way parallel E2E shards in ci:local Replaces the single postgres service with 4 (postgres-1..4) on host ports 5434-5437. scripts/ci-local.sh fans 4 workers via xargs -P4 inside the runner container; each pinned to its own DATABASE_URL via SHARD=N/4. Wall-time on a 16-core host: ~6 min sequential -> ~1.5-2 min sharded. Total full-gate wall-time goes from ~25 min to ~3-5 min warm. Also handles git-worktree (Conductor) layouts: when /app/.git is a file instead of a directory, parse the gitdir + commondir and bind-mount the shared host gitdir at its absolute path. Without this, in-container `git ls-files` (used by scripts/check-trailing-newline.sh and friends) exits 128 with "not a git repository". Also runs `git config --global --add safe.directory '*'` inside the container so the root-uid container can read host-uid gitdir without "dubious ownership" rejection. CHANGELOG entry updated to cover the speedup. - docker-compose.ci.yml: 4 pgvector services + per-shard named volumes - scripts/ci-local.sh: parallel xargs orchestration + worktree mount fix - CHANGELOG.md v0.23.1: 4-way sharded wall-time, 36 E2E files, --no-shard flag * chore: regenerate llms-full.txt for v0.23.1 doc updates Required by test/build-llms.test.ts case 4 — committed llms-full.txt must match `bun run build:llms` output. The CHANGELOG + CLAUDE.md updates in this branch shifted bytes; regen catches up. * feat: scripts/run-unit-shard.sh + slow-test convention Tier 1 + Tier 4 plumbing: - scripts/run-unit-shard.sh: SHARD=N/M filter for unit files (excludes test/e2e/*). Excludes *.slow.test.ts (Tier 4 convention) so the fast shard fan-out skips known-slow files; CI's `bun run test` still includes them via default discovery. - scripts/run-slow-tests.sh: companion that runs ONLY *.slow.test.ts. Wired as `bun run test:slow`. - scripts/profile-tests.sh: portable awk parser that extracts the top-N slowest tests from any captured `bun test` output. Wired as `bun run test:profile`. Use it to pick demotion candidates. * feat: PGLite snapshot fixture for ~4.5x faster cold init (Tier 3) scripts/build-pglite-snapshot.ts boots a fresh PGLite, runs the full initSchema() (forward bootstrap + 30 migrations), and dumps the post-init state to test/fixtures/pglite-snapshot.tar plus a SHA-256 schema hash sidecar (.version). Both gitignored — built on demand via `bun run build:pglite-snapshot`. PGLiteEngine.connect() reads GBRAIN_PGLITE_SNAPSHOT env: validates the sidecar hash against the in-process MIGRATIONS hash, loads via PGLite's loadDataDir blob, sets _snapshotLoaded so initSchema() short-circuits. Measured per-file cold init drops from 828ms → 181ms. Bootstrap-correctness tests (bootstrap.test.ts, schema-bootstrap-coverage.test.ts) explicitly delete the env at file top so they keep exercising the cold path they verify. * feat: --classify-only + heartbeat tolerance fix (Tiers 2 + flake fix) - scripts/select-e2e.ts: --classify-only flag emits EMPTY|DOC_ONLY|SRC. Used by ci-local.sh's --diff fast-path to skip the heavy gate when only docs changed. - test/progress.test.ts: startHeartbeat tolerance widened to 1-20 over 200ms (was 2-6 over 85ms). Under 4-way parallel shard load on a contended host, setTimeout's effective quantum balloons and the tight bound flakes. The test still verifies "fires multiple times, stops cleanly" — exact count was never load-bearing. * feat: 4-way unit + E2E sharding in ci-local.sh + CHANGELOG (Tiers 1-4) ci-local.sh ties the four tiers together: - Tier 2: pre-flight diff classification on host. DOC_ONLY exits in ~5s (gitleaks only, no postgres, no container). - Tier 1: guards + typecheck run ONCE before fan-out. xargs -P4 then spawns 4 shards inside the runner container, each running unit phase (env -u DATABASE_URL bash run-unit-shard.sh) followed by E2E phase (DATABASE_URL=postgres-N bash run-e2e.sh) — both sharded N/4. Per-shard logs in /tmp/shard-logs/shard-N.log; printed in shard order at the end. - Tier 3: snapshot fixture built once at runner startup if missing, GBRAIN_PGLITE_SNAPSHOT exported so all shards inherit. - Tier 4: run-unit-shard.sh excludes *.slow.test.ts; run-slow-tests.sh + test:slow npm script handle the demoted set. - --no-shard preserves the legacy single-process flow for debug. package.json: build:pglite-snapshot, test:slow, test:profile scripts. Measured wall-time on 16-core host: 100s warm (down from ~22 min cold single-process). 4 shards × ~640-1024 unit tests each, plus 9 E2E files each. PGLite snapshot saves 4.5× per cold init (828ms → 181ms). CHANGELOG.md updated with measured numbers + four-tier breakdown. --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…rdict model tests (#527) * v0.23.1 fix: dream self-consumption guard + configurable verdict model Built-in isDreamOutput() guard in transcript-discovery.ts auto-skips any transcript whose first 2000 chars contain dream output slug prefixes (wiki/personal/reflections/, wiki/originals/ideas/, wiki/personal/patterns/, dream-cycle-summaries/). Prevents infinite recursion if dream output is ever fed back into the corpus. judgeSignificance() now accepts a verdictModel parameter, loaded from dream.synthesize.verdict_model config key. Default: claude-haiku-4-5. 3 new test cases covering the guard. * feat(dream): replace content-prefix guard with orchestrator-stamped marker The v0.23.1 prefix-string guard had two flaws caught by codex review. serializeMarkdown does not embed the page slug into body content, so the heuristic could miss real dream output. And real conversation transcripts often cite brain slugs ("earlier I wrote about wiki/personal/reflections/identity..."), so the heuristic dropped legitimate transcripts silently. Swap content inference for explicit identity. renderPageToMarkdown and writeSummaryPage now stamp `dream_generated: true` + `dream_cycle_date` into frontmatter at render time. Guard checks for the marker via DREAM_OUTPUT_MARKER_RE (anchored at frontmatter open, BOM/CRLF tolerant, scans first 2000 chars, word boundary on `true`). Cannot drift, cannot false-positive on user text, cannot miss real output. Tests built from a real Page → renderPageToMarkdown → isDreamOutput round-trip (codex finding #5 — synthetic strings don't prove the guard catches what synthesize actually produces). Coverage: regression fixture, false-positive prevention on user transcripts citing slugs, CRLF+BOM, whitespace/case variants, anchor-at-byte-0, perf bound, bypass plumbing, dream_generatedfoo word-boundary check. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(dream): --unsafe-bypass-dream-guard CLI flag Explicit opt-in to disable the synthesize self-consumption guard. The flag is intentionally NOT tied to --input — codex review caught that implicit bypass is a footgun: any caller could synthesize a dream- generated page directly via --input, get a cached positive verdict, and silently re-trigger the loop bug. Plumbing: dream.ts CLI parses the flag → DreamArgs.bypassDreamGuard → runCycle({ synthBypassDreamGuard }) → SynthesizePhaseOpts.bypassDreamGuard → discoverTranscripts({ bypassGuard }) and readSingleTranscript. Loud stderr warning at phase entry when set so the cost is visible. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * v0.23.2 chore: bump version + CHANGELOG for corrected guard architecture Replaces the v0.23.1 release notes with the v0.23.2 voice describing the orchestrator-stamped marker approach and the --unsafe-bypass-dream-guard flag. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: sync project docs for v0.23.2 marker-based guard Update CLAUDE.md Key Files entries for src/core/cycle/synthesize.ts, src/core/cycle/transcript-discovery.ts, and src/commands/dream.ts to reflect the v0.23.2 dream_generated frontmatter marker that replaces the v0.23.1 content-prefix self-consumption guard, plus the new --unsafe-bypass-dream-guard CLI flag. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * docs: regenerate llms-full.txt for v0.23.2 CLAUDE.md updates CI's `build-llms generator > committed match generator output` guard caught drift after the v0.23.2 doc-sync (commit 507edb1) updated three Key Files entries in CLAUDE.md without re-running `bun run build:llms`. The llms.txt index didn't drift (no new doc URLs); only the inlined llms-full.txt bundle needed refreshing. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * test(e2e): round-trip dream-recursion coverage for v0.23.2 marker guard Three new PGLite E2E cases exercise the actual production loop scenario end-to-end. Unit tests covered the bug class at the function-pair level (renderPageToMarkdown → readSingleTranscript). These cover it at the phase level: runPhaseSynthesize with a real engine, real putPage, real renderPageToMarkdown, real corpus-dir discovery. 1. Leaked dream output is skipped on next synthesize run. The reflection page is inserted, reverse-rendered (which stamps `dream_generated: true`), dropped into the corpus dir as .txt, and the next phase run reports "no transcripts to process" with a stderr skip log. Verdict cache stays untouched so a future legit edit isn't shadowed by a stale cached "false". 2. bypassDreamGuard=true at phase entry re-enables ingestion. Same marked file gets discovered through the loud-warning path. Proves --unsafe-bypass-dream-guard plumbing reaches discoverTranscripts at phase scope. 3. Mixed corpus (leaked dream output + real conversation transcript) discovers exactly the real one. Pins codex finding #1's headline false-positive case: a transcript citing wiki/personal/reflections/ in body must NOT be skipped. Stderr capture via process.stderr.write spy with try/finally restore. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(test): use valid PageType 'note' in round-trip E2E fixtures CI typecheck caught three TS2322 violations in the round-trip E2E fixtures: 'reflection' is not a member of PageType. Reflections are filed as 'note' in production (renderPageToMarkdown falls back to 'note' for unknown types). No behavior change — the guard test still exercises the same serializeMarkdown → discoverTranscripts loop. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs(claude): require `bun run typecheck` before push The pre-ship section listed `bun test` as the unit-test path but didn't flag the trap: `bun test` (the bun runner) does NOT run TypeScript type checking. Only `bun run test` (the npm script) does, because it chains `bun run typecheck` + the four shell pre-checks before the runner. CI on PR #527 caught a `'reflection'` literal that `PageType` doesn't admit (PageType is a closed union). The runtime E2E and `bun test` both passed locally because the runner doesn't gate on TS. The separate typecheck stage in CI rejected it. New rule: run `bun run typecheck` (or `bun run test`, which wraps it, or `bun run ci:local` for the full gate) before pushing. The runner- alone path is for hot-loop test iteration only. Also regenerated llms-full.txt for the CLAUDE.md update. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Wintermute <wintermute@garrytan.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: v0.19.0 — skillify loop + AGENTS.md compat + brain-first convention This is the v0.19.0 release. The branch ships four new CLI commands, a refactor to check-resolvable, and an expansion of the brain-first convention for sub-agent tool discovery. The original commit message described only the convention expansion, undercounting the scope by ~5x; this amend captures the full release. NEW COMMANDS - gbrain skillify scaffold <name> — 4 stub files + idempotent resolver row - gbrain skillify check [path] — 10-item post-task audit (promoted) - gbrain skillpack list / install — curated 25-skill bundle, atomic install - gbrain skillpack diff <name> — per-file diff preview - gbrain routing-eval — dedicated CI verb for Check 5 fixtures CHECK-RESOLVABLE REFACTOR - Accepts AGENTS.md as a resolver file alongside RESOLVER.md, at either the skills directory or one level up (workspace root layout). - Auto-derives the skill manifest by walking skills/*/SKILL.md when manifest.json is missing. - Splits ResolvableReport into errors[] + warnings[] so advisory checks (filing audit, routing gaps, DRY violations) don't break CI by default. - New --strict opt-in flag promotes warnings to exit 1. BRAIN-FIRST CONVENTION - skills/conventions/brain-first.md expanded from 5-step lookup guide to full sub-agent reference: tool inventory, lookup chain, score thresholds, authority hierarchy, sync rules, entity page conventions, sub-agent propagation rule. PRODUCTION-READINESS HARDENING (this branch's review pass) - routing-eval --llm: emits stderr placeholder notice + runs structural layer only. README, CHANGELOG, CLI help all rewritten consistently. Was a silent no-op against documented contract. - skillpack installer: receipt comment in fence (cumulative-slugs="...") preserves single-skill-install accumulation while letting install --all prune removed bundle skills cleanly. Unknown rows preserved + stderr warning for the operating agent. Pre-v0.19 fences upgrade silently. - skillify scaffold: resolver-row regex broadened to detect backticked, quoted, and bare path forms. No duplicate row on --force after the user normalizes formatting. - scripts/check-privacy.sh: now wired into package.json test chain so the wintermute-ban rule is actually enforced. New regression test. - E2E Tier 2 (LLM skills) promoted from schedule-only to required per-PR CI. Local Tier 1 + Tier 2 verified clean. - Stale v0.17/v0.18 version labels rewritten across new files. TESTS - test/routing-eval-cli.test.ts: 4 cases covering --llm warn semantics - test/privacy-script-wired.test.ts: regression guard for CI wiring - test/skillpack-install.test.ts: 4 new cases for receipt + cumulative + unknown-row preserve+warn + pre-v0.19 upgrade path - test/skillify-scaffold.test.ts: 4 new cases for broadened regex VERIFICATION - bun test: 2237 pass / 18 known PGLite-contention flakes (CI green; documented as P3 dev-experience in TODOS.md) - bun run typecheck: clean - bun run test:e2e: 18/19 files green (1 pre-existing flake on master, not caused by this branch — verified via git stash) - llms.txt + llms-full.txt regenerated to match README + CHANGELOG Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix: scrub banned fork name from public artifacts The privacy guard wired into the test chain in this branch caught 5 pre-existing references to the banned OpenClaw fork name in CHANGELOG.md (2x), skills/migrations/v0.19.0.md (1x), src/cli.ts (1x), and src/commands/sync.ts (1x). All originated in master's v0.19.0 release notes and migration doc when the privacy script existed but wasn't wired into CI yet. Replacements per CLAUDE.md privacy mapping: - Origin-story copy (CHANGELOG layer narratives, code comments naming the production deployment that drove the feature) → "Garry's OpenClaw" - Reader-facing migration step → "your OpenClaw" No code semantics changed. Comments + headings only. Verification: scripts/check-privacy.sh exits 0, full CI guard chain green (privacy + jsonb + progress + wasm + typecheck). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore: bump VERSION to 0.24.0 + new CHANGELOG entry Bump branch version above master's v0.21.0 per CLAUDE.md "CHANGELOG + VERSION are branch-scoped" rule. The new v0.24.0 entry at the top of CHANGELOG covers what THIS branch adds vs master: - routing-eval --llm honesty pass (4-surface contract drift fix) - skillpack installer cumulative-receipt + unknown-row preserve+warn (the Codex-caught regression that would have shipped in master if the original v0.19.0 had landed without this branch's review pass) - skillify scaffold resolver-row regex broadening (backtick + quoted + bare forms; idempotency contract preserved under hand-editing) - 5 banned-name leaks scrubbed from public artifacts - check-privacy.sh wired into CI test chain + regression guard test - 7 stale v0.17/v0.18 version labels rewritten across 5 files - Tier 2 (LLM-skills E2E) promoted from schedule-only to required per-PR VERSION 0.21.0 → 0.24.0 package.json version field synced. llms.txt + llms-full.txt regenerated (no content drift; sizes match). Test suite: 62/62 green across the 5 test files this branch added or extended (routing-eval-cli, privacy-script-wired, skillpack-install, skillify-scaffold, build-llms). CI guards: privacy + jsonb + progress + wasm + typecheck all clean. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: update project documentation for v0.24.0 Auto-discovered drift via /document-release after the v0.24.0 hardening pass landed. All factual corrections clearly warranted by the diff. CLAUDE.md: - Skillpack installer: documented the cumulative-slugs receipt comment, install --all prune semantics, unknown-row preserve+warn behavior, and pre-v0.24 silent upgrade. Was previously vague about "tracks a skill manifest so install --update diffs cleanly" without explaining what the receipt is or why it matters. - routing-eval: replaced the false claim that --llm "opts into a Haiku tie-break layer for CI." Now correctly describes the placeholder semantic landed in v0.24.0 (stderr notice + structural-only run). README.md: - Skillpack section: added one paragraph on the receipt comment + the user-visible stderr message for hand-added rows. Connects the safe rerun promise to the v0.24.0 implementation that actually enforces it. CONTRIBUTING.md: - Running tests section: now recommends `bun run test` (full CI guard chain + typecheck + tests) before pushing. Names each guard so new contributors understand what catches what. The privacy guard (newly wired in v0.24.0) is one of these — without `bun run test` you'd skip it locally and find out from CI. llms-full.txt: regenerated to reflect CLAUDE.md changes. Verification: full guard chain green locally (privacy + jsonb + progress + wasm + typecheck). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Garry Tan <garry@ycombinator.com> Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Qodo-Free-For-OSS · 2026-05-01T08:06:07Z

Hi, The self-healing UPDATE casts the job_id filter parameter to int[], but subagent_tool_executions.job_id is BIGINT; this will throw "integer out of range" when job IDs exceed 32-bit and will break synthesize/patterns provenance collection.

Severity: action required | Category: correctness

How to fix: Use bigint[] for job_id

Agent prompt to fix - you can give this to your LLM of choice:

Issue description

The self-healing UPDATE in dream-cycle slug provenance uses job_id = ANY($1::int[]), but subagent_tool_executions.job_id is BIGINT. This can crash with integer out of range when job IDs exceed 32-bit.

Issue Context

The dream phases rely on this UPDATE to repair pre-v0.23.1 double-encoded jsonb strings so input->>'slug' works.

Fix Focus Areas

src/core/cycle/synthesize.ts[448-467]

src/core/cycle/patterns.ts[222-241]

Change casts to $1::bigint[] (or remove the cast if the driver reliably binds as bigint array), and ensure the SELECT that follows still uses the same type.

We noticed a couple of other issues in this PR as well - happy to share if helpful.

Found by Qodo code review. FYI, Qodo is free for open-source.

…ct test (#437) * feat(v0.22.0): eval_candidates + eval_capture_failures schema (Lane 1A) R1 substrate for BrainBench-Real, replayed onto master after Cathedral II landed. Migration v30 (slotted after master's v25-v29 Cathedral II wave) creates two tables: eval_candidates: per-call capture of MCP/CLI/subagent query+search traffic. Column set lets gbrain-evals replay with full fidelity — source_ids from v0.18 multi-source, vector_enabled/detail_resolved/ expansion_applied so replay knows what hybridSearch actually did, remote + job_id + subagent_id so rows are traceable to their origin. query is CHECK-capped at 50KB; PII scrubber (Lane 1B) runs before insert. eval_capture_failures: cross-process audit trail. In-process counters don't work because `gbrain doctor` runs in a separate process from the MCP server. Persistent rows let doctor query capture health via COUNT(*) GROUP BY reason over the last 24h. Both tables get RLS on Postgres gated on BYPASSRLS (matches v24/v29 posture). PGLite ignores RLS; sqlFor split carries only DDL. 5 new BrainEngine methods (breaking-interface addition, drives v0.22.0 minor bump): logEvalCandidate, listEvalCandidates, deleteEvalCandidatesBefore, logEvalCaptureFailure, listEvalCaptureFailures. listEvalCandidates uses ORDER BY created_at DESC, id DESC so `gbrain eval export` is deterministic across same-millisecond inserts. Also adds HybridSearchMeta type for the side-channel callback used by Lane 1C's op-layer capture (no change to hybridSearch return shape — that respects Cathedral II's existing SearchResult[] contract). Tests: 14 PGLite round-trip cases + 8 v30 structural assertions. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.22.0): PII scrubber + op-layer capture module (Lane 1B) Replayed onto master post-Cathedral II. Same semantics as the original v0.21.0 work — only adjusted to import HybridSearchMeta from types.ts (canonical home) instead of redeclaring it locally. src/core/eval-capture-scrub.ts — pure-function regex scrubber with 6 pattern families: emails, phones (US + E.164), SSN (year-aware), Luhn-verified credit cards, JWT-shaped tokens, bearer tokens. Zero deps. Adversarial-input safe. src/core/eval-capture.ts — op-layer hook helper: - buildEvalCandidateInput(ctx, {scrub_pii}) — pure row builder - classifyCaptureFailure(err) — Postgres SQLSTATE → reason tag - captureEvalCandidate(engine, ctx, opts) — best-effort, never throws - isEvalCaptureEnabled / isEvalScrubEnabled — file-plane config checks GBrainConfig gains `eval?: {capture?, scrub_pii?}`. Both default ON. File-plane only — `gbrain config set` writes the DB plane, doesn't control capture. Tests: 17 scrubber + 21 capture-module cases. Zero regressions. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.22.0): hybridSearch onMeta callback + op-layer capture (Lane 1C) Replayed onto master. Adapted from the original v0.21.0 work to keep Cathedral II's contract intact: hybridSearch's return stays `Promise<SearchResult[]>` (unchanged), and meta surfaces via an optional `onMeta?: (meta: HybridSearchMeta) => void` callback in HybridSearchOpts. Cathedral II callers leave onMeta undefined and pay no cost. The op-layer capture wrapper passes a closure that threads meta into the captured row so gbrain-evals can distinguish: - "with OPENAI_API_KEY" vs "keyword-only fallback" (vector_enabled) - "expansion fired" vs "expansion requested + silently fell back" (expansion_applied) - what hybridSearch actually used after auto-detect (detail_resolved) Op-layer capture wired into both `query` and `search` op handlers in src/core/operations.ts. Single hook site catches MCP dispatch + CLI + subagent tool-bridge from the same place. Fire-and-forget, never throws, respects ctx.config.eval.capture off-switch. Tests: - test/hybrid-meta.test.ts (8 cases) — onMeta accuracy across the 4 return paths in hybridSearch + verification that omitting onMeta leaves Cathedral II callers unchanged. - test/mcp-eval-capture.test.ts (10 cases) — query/search ops capture correctly with MCP/CLI/subagent contexts, scrub on/off, capture=false off-switch, non-captured ops (list_pages, get_page), F1 failure isolation. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.22.0): gbrain eval export/prune + doctor eval_capture check (Lane 1D) Replayed onto master. Same semantics as the original v0.21.0 work. CLI: gbrain eval export [--since DUR] [--limit N] [--tool query|search] NDJSON to stdout, every row prefixed with "schema_version":1 per docs/eval-capture.md contract. EPIPE-safe streaming, stderr heartbeats, deterministic ordering (created_at DESC, id DESC). gbrain eval prune --older-than DUR [--dry-run] Explicit retention cleanup. Requires --older-than (never deletes without a window). Duration strings: 30d, 7d, 1h, 90m, 3600s. Legacy bare `gbrain eval --qrels …` still works via sub-subcommand fall-through. gbrain doctor gains an eval_capture check between markdown_body_completeness and queue_health: reads eval_capture_failures for the last 24h, groups by reason, warns when non-zero. Pre-v30 brains get "Skipped (table unavailable)" — non-fatal. docs/eval-capture.md ships the stable NDJSON schema reference for gbrain-evals consumers. Tests: 9 export cases + 5 prune cases. Doctor check covered by existing doctor tests on master. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.22.0): public-exports contract test + CI count guard (Lane 2 / R2) Master locks 17 public subpath exports as gbrain's stable third-party contract. Zero enforcement existed. This PR locks the surface in two layers: 1. test/public-exports.test.ts — runtime contract test. Reads package.json "exports" at startup. For each subpath, imports via the package name ("gbrain/engine"), NOT the relative filesystem path — that's the difference between exercising the actual resolver and bypassing it. Every subpath gets a canary symbol pinned (e.g. gbrain/search/hybrid must export hybridSearch + rrfFusion) so a refactor that renames or removes one fails CI before downstream consumers (gbrain-evals) silently break. 2. scripts/check-exports-count.sh — CI structural guard. Wired into `bun test` after check-jsonb-pattern.sh + check-progress-to-stdout.sh + check-wasm-embedded.sh per master's precedent. EXPECTED_COUNT=17 baseline — shrinks fail loudly, growth also fails so the new canary must be pinned in the runtime test deliberately. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs+e2e(v0.22.0): VERSION/CHANGELOG/CLAUDE/README + Postgres E2E (Lane 3) Bump VERSION + package.json to 0.22.0 (next free slot after master's v0.21.0 Code Cathedral II minor). CHANGELOG.md v0.22.0 entry follows the Garry voice template: - Bold 2-line headline - Lead paragraph contextualizing v0.20 + v0.21 + v0.22 progression - Numbers-that-matter table comparing v0.21.0 → v0.22.0 - "What this means for you" sectioned by audience - "## To take advantage of v0.22.0" operator runbook - Itemized changes CLAUDE.md updates: - Key files: 8 new module entries (eval-capture*, eval-export, eval-prune, docs/eval-capture.md, public-exports test). hybrid.ts entry rewritten to reflect the additive `onMeta` callback (return shape unchanged). - Key commands: new v0.22.0 section for `gbrain eval export`, `gbrain eval prune`, and the doctor `eval_capture` check, with the file-plane vs DB-plane config gotcha called out. README.md: one-paragraph pointer after the BrainBench blurb so anyone reading the landing page sees the new session-capture feature. llms.txt + llms-full.txt regenerated to pick up the doc additions. test/e2e/eval-capture.test.ts (Postgres-only E1 spec): - CHECK violation surfaces as Postgres SQLSTATE 23514 on oversize input - RLS is actually enabled on both eval_candidates + eval_capture_failures - 50 concurrent logEvalCandidate calls — no deadlock, all distinct IDs Skips gracefully when DATABASE_URL is unset. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs(todos): P0 — PGLite test-runner concurrency flake Pre-existing on master, surfaces ~27 false failures when bun test runs all 174 files together. Each failing file passes in isolation. Tracked for a dedicated investigation branch. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(v0.22.0): adversarial review post-fixes (doctor RLS, onMeta safety) Two surgical fixes from /ship adversarial review, plus 6 follow-ups TODO'd into v0.22.1: - doctor.ts: distinguish pre-v30 missing-table (42P01, ok skip) from RLS-denied SELECT (42501, warn) and other DB errors (warn). The check exists specifically to surface capture-failure misconfigs cross-process, so silently reporting "ok / skipped" on the most diagnostic class defeated the purpose. - hybrid.ts: wrap onMeta invocation in try/catch via small emitMeta helper. The callback is part of the public gbrain/search/hybrid contract; a throwing user-supplied closure must never break the search hot path. - TODOS.md: 6 P1 follow-ups (eval prune real COUNT, scrubber CC false positives, dead 'scrubber_exception' enum value, id-cursor for cross-window dedup, public-export canary pinning, EXPECTED_COUNT dedup). - TODOS.md: P0 entry for the pre-existing PGLite test-runner concurrency flake (~27 false failures in full bun test on master). - CHANGELOG.md: 2 bullets noting the doctor + onMeta hardening. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * chore(version): bump v0.22.0 → v0.25.0 (queue-aware version pick) Master is at v0.21.0. Open PRs claim v0.21.1 (#432) and v0.24.0 (#387). v0.25 is the first uncontested slot, so this branch claims it. Pure rename across VERSION, package.json, CHANGELOG header, and every "v0.22.0" reference in CLAUDE.md / README.md / TODOS.md / docs/eval-capture.md / src/ / test/ files. CHANGELOG date bumped to 2026-04-26. llms.txt + llms-full.txt regenerated. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.25.0): gbrain eval replay + contributor doc + CONTRIBUTING link Closes the gap between "session capture works" (this PR's core) and "contributors actually use it before merging." Three artifacts: - src/commands/eval-replay.ts (~340 LOC) — reads NDJSON from `gbrain eval export`, re-runs each captured query/search against the current brain, computes set-Jaccard@k, top-1 stability, and latency delta. Stable JSON shape (schema_version:1) for CI gating; human mode prints a regression table sorted worst-first. Pure Bun, zero new deps. Stub-engine tests cover Jaccard math, NDJSON parser (including v2 forward-compat rejection + line-numbered errors), --limit, --verbose, --json, and graceful per-row error handling. 16/16 passing. - docs/eval-bench.md (~80 lines) — contributor guide. The 4-command loop (export → change → replay → diff), metric definitions with healthy ranges (Jaccard ≥0.85, top-1 ≥85%, latency Δ within ±50ms), trigger paths, CI integration snippet, hand-crafted NDJSON corpus path for fresh installs, and the off-switch. Pairs with the existing docs/eval-capture.md which is the consumer-facing wire format. - CONTRIBUTING.md gains a "Running real-world eval benchmarks (touching retrieval code)" section with the trigger paths and a link to docs/eval-bench.md. Reviewers now have a one-line ask: "did you run replay?" CLAUDE.md key files updated. CHANGELOG bullets added. llms.txt regenerated. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * feat(v0.25.0): CONTRIBUTOR_MODE flag — capture off by default for users Eval capture was on for everyone in the v0.25.0 draft. Privacy footgun: end users had retrieval traffic accumulate in their brain DB without asking, even with PII scrubbing. Flips to off by default + explicit opt-in for contributors who actually use the replay loop. Resolution order in isEvalCaptureEnabled(): 1. config.eval.capture === true → on 2. config.eval.capture === false → off 3. process.env.GBRAIN_CONTRIBUTOR_MODE === '1' → on 4. otherwise → off The env var is the contributor-facing toggle (one line in .zshrc, no JSON edit). Explicit config wins both directions for users who want to override per-brain. PII scrubbing gate stays independent — default true regardless of CONTRIBUTOR_MODE — so any brain that does capture still scrubs. Tests rewritten: env var hygiene per-test (origMode preserved + restored in finally). 9/9 pass; total v0.25.0 suite is 198/198. Docs: - README.md gains a Contributing-section pointer to the env var. - CONTRIBUTING.md gains a "CONTRIBUTOR_MODE — turn on the dev loop" section with verification commands and resolution-order table. - docs/eval-bench.md leads with the prerequisite (must set the env var for the rest of the doc to be useful). - docs/eval-capture.md "Config" section split into Path A (env var) + Path B (config) with explicit resolution-order rules. - CHANGELOG v0.25.0 entry corrected ("on by default" was wrong) plus a new top itemized bullet calling out the gate change. - CLAUDE.md eval-capture entry annotated with the new gate logic. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs: post-ship documentation pass for v0.25.0 Cross-references every doc against the final state of the branch (CONTRIBUTOR_MODE flag, eval replay tool, off-by-default capture): - README.md: top callout rewritten — was implying capture-on-by-default contradicting the gate landed in 7a80ce2. Now leads with "contributor opt-in" and links docs/eval-bench.md alongside docs/eval-capture.md. - AGENTS.md: new "Eval retrieval changes" task entry with the CONTRIBUTOR_MODE+replay one-liner so non-Claude agents (Codex, Cursor, Aider) have the same path. - CLAUDE.md: "Key commands added in v0.25.0" gains the replay command and a CONTRIBUTOR_MODE bullet covering the resolution order. - CHANGELOG.md: headline rewritten to match the actual feature ("benchmark retrieval changes against real captured queries before merging" — was "every real query is captured"). Stale "v0.22 ships the substrate" → v0.25. Test count corrected 82 → 144 (added 16 replay + 9 CONTRIBUTOR_MODE + 8 v31-shape tests since the original count). Two metric rows added to the numbers table: default-off posture, in-tree replay tooling. "To take advantage" block split into user vs contributor branches with shell-rc instructions. - TODOS.md: v0.22.1 follow-up reference corrected to v0.25.1. llms.txt + llms-full.txt regenerated. Typecheck clean. 198/198 v0.25.0 tests still green. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…n/gbrain into fix/dream-jsonb-and-lock

…nb + doctor The four `subagent_*` jsonb writers in `src/core/minions/handlers/subagent.ts` (persistMessage, persistToolExecPending, persistToolExecComplete, persistToolExecFailed) used `engine.executeRaw` with `JSON.stringify(value)` plus `$N::jsonb` cast. On the postgres-engine path that goes through postgres.js's `unsafe()`, that combination produces a jsonb string scalar instead of an object — exactly the v0.12.0 double-encode shape, on a second set of tables. Verified empirically (probe inside this branch, not committed): P1 JSON.stringify(obj) + $::jsonb → jsonb_typeof='string' (broken) P3 raw object + $::jsonb → jsonb_typeof='object' (correct) P4 sql.json(obj) via unsafe → jsonb_typeof='object' (correct) The four call sites are changed to pass the raw value. postgres.js v3 auto-encodes objects/arrays for jsonb columns (already what queue.ts:233 relies on for `minion_jobs.data`, never broken). PGLite handles raw values identically (verified — all three patterns produce object jsonb on PGLite). Existing data on the user's brain at the time of fix: subagent_messages.content_blocks: 40/40 corrupt subagent_tool_executions.input: 39/39 corrupt subagent_tool_executions.output: 39/39 corrupt All 118 rows repaired by `gbrain repair-jsonb` after extending TARGETS. Symptom this resolves: dream synthesize's orchestrator (`collectChildPutPageSlugs` in src/core/cycle/synthesize.ts:459) queries `input->>'slug'` to gather slugs the subagent wrote; on string-typed jsonb that operator returns NULL, so `pages_written` reports 0 even when child subagents successfully wrote pages. The reverse-write step that mirrors DB → markdown is then skipped, leaving real synthesized pages stranded in the DB. After this fix, the orchestrator picks up slugs correctly and the full dream cycle closes the loop. Companion changes: - `repair-jsonb` extended from 5 → 8 columns (subagent_messages.content _blocks, subagent_tool_executions.{input,output}); guards each target with `to_regclass()` so pre-v0.15 brains that lack the subagent_* tables don't throw at upgrade time. - `doctor`'s `jsonb_integrity` check extended to the same 8 columns with the same guard. Any future user hitting this bug from upstream master gets a clear "X rows double-encoded ... Fix: gbrain repair-jsonb" warning instead of silent dream failures. - `repair-jsonb.ts` header comment retracted: the prior claim that parameterized `$N::jsonb` was always safe was wrong; safety came from queue.ts/etc. passing raw objects, not from the binding form. Upstream history: PR garrytan#525 was a chmod fix mis-attributed by local commits; the real outstanding upstream PR is garrytan#539 (zombie lock + post-hoc data repair via UPDATE) which does NOT patch the write path. Master HEAD still ships the buggy form. This patch is upstream-worthy as a follow-up to Tests: 245 pass across minions, subagent-handler, cycle-synthesize, cycle-patterns, repair-jsonb, migrations-v0_12_2, and doctor. typecheck clean.

garrytan · 2026-05-24T08:07:22Z

Closing as superseded — the work in this PR mostly shipped in two follow-on waves: v0.23.2 closed the synthesize-phase orchestrator slug-collection bug (dream_generated frontmatter marker in renderPageToMarkdown + isDreamOutput guard in transcript-discovery.ts), and v0.28.1 added the zombie-reap layer (installSigchldHandler() in src/core/zombie-reap.ts + tini-as-PID-1 wrapping in supervisor.ts). The 8253-line branch is too stale to land as-is against current master, but the core fixes are in. Thanks for the load-bearing diagnosis.

…nb + doctor The four `subagent_*` jsonb writers in `src/core/minions/handlers/subagent.ts` (persistMessage, persistToolExecPending, persistToolExecComplete, persistToolExecFailed) used `engine.executeRaw` with `JSON.stringify(value)` plus `$N::jsonb` cast. On the postgres-engine path that goes through postgres.js's `unsafe()`, that combination produces a jsonb string scalar instead of an object — exactly the v0.12.0 double-encode shape, on a second set of tables. Verified empirically (probe inside this branch, not committed): P1 JSON.stringify(obj) + $::jsonb → jsonb_typeof='string' (broken) P3 raw object + $::jsonb → jsonb_typeof='object' (correct) P4 sql.json(obj) via unsafe → jsonb_typeof='object' (correct) The four call sites are changed to pass the raw value. postgres.js v3 auto-encodes objects/arrays for jsonb columns (already what queue.ts:233 relies on for `minion_jobs.data`, never broken). PGLite handles raw values identically (verified — all three patterns produce object jsonb on PGLite). Existing data on the user's brain at the time of fix: subagent_messages.content_blocks: 40/40 corrupt subagent_tool_executions.input: 39/39 corrupt subagent_tool_executions.output: 39/39 corrupt All 118 rows repaired by `gbrain repair-jsonb` after extending TARGETS. Symptom this resolves: dream synthesize's orchestrator (`collectChildPutPageSlugs` in src/core/cycle/synthesize.ts:459) queries `input->>'slug'` to gather slugs the subagent wrote; on string-typed jsonb that operator returns NULL, so `pages_written` reports 0 even when child subagents successfully wrote pages. The reverse-write step that mirrors DB → markdown is then skipped, leaving real synthesized pages stranded in the DB. After this fix, the orchestrator picks up slugs correctly and the full dream cycle closes the loop. Companion changes: - `repair-jsonb` extended from 5 → 8 columns (subagent_messages.content _blocks, subagent_tool_executions.{input,output}); guards each target with `to_regclass()` so pre-v0.15 brains that lack the subagent_* tables don't throw at upgrade time. - `doctor`'s `jsonb_integrity` check extended to the same 8 columns with the same guard. Any future user hitting this bug from upstream master gets a clear "X rows double-encoded ... Fix: gbrain repair-jsonb" warning instead of silent dream failures. - `repair-jsonb.ts` header comment retracted: the prior claim that parameterized `$N::jsonb` was always safe was wrong; safety came from queue.ts/etc. passing raw objects, not from the binding form. Upstream history: PR garrytan#525 was a chmod fix mis-attributed by local commits; the real outstanding upstream PR is garrytan#539 (zombie lock + post-hoc data repair via UPDATE) which does NOT patch the write path. Master HEAD still ships the buggy form. This patch is upstream-worthy as a follow-up to Tests: 245 pass across minions, subagent-handler, cycle-synthesize, cycle-patterns, repair-jsonb, migrations-v0_12_2, and doctor. typecheck clean.

Wintermute added 2 commits April 30, 2026 18:35

garrytan force-pushed the fix/dream-jsonb-and-lock branch from cfd782e to f443c2e Compare April 30, 2026 18:35

garrytan and others added 3 commits April 30, 2026 20:47

garrytan and others added 3 commits May 1, 2026 09:02

oppo: track teddy blank thread hostiles

f1ad0d1

Merge branch 'fix/dream-jsonb-and-lock' of https://github.com/garryta…

6a96925

…n/gbrain into fix/dream-jsonb-and-lock

vinsew mentioned this pull request May 3, 2026

fix(subagent): drop JSON.stringify on jsonb writes (orchestrator slug-collection bug) #597

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fix: zombie PID lock detection + self-healing jsonb repair in dream cycle#539

fix: zombie PID lock detection + self-healing jsonb repair in dream cycle#539
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Fix 1: Remove JSON.stringify() from persist functions (already on master, 80b3909)

Fix 2: Self-healing jsonb repair in collectChildPutPageSlugs (this PR)

Fix 3: Zombie PID detection in cycle lock acquisition (this PR)

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garrytan commented Apr 30, 2026 •

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Fix 1: Remove JSON.stringify() from persist functions (already on master, `80b3909`)