fix: 8 root-cause fixes from /investigate (v0.14.2) (#259)

* fix: 8 root-cause fixes from /investigate wave

Consolidated bundle of bug fixes from /investigate on the 8 deferred bugs.
Each fix was designed to go at the structural gap, not the symptom. Codex
verified 20 load-bearing claims on the plan; 12 triggered plan revisions.

Bug 2  — GBRAIN_POOL_SIZE env knob + init finally blocks (no auto-detect).
         Covers both the singleton pool (db.ts) and instance pool (import.ts:140).
Bug 3  — Centralize migration ledger writes in apply-migrations runner.
         Removed appendCompletedMigration from v0_11_0, v0_12_0, v0_12_2,
         v0_13_0, v0_13_1. Added 3-partial wedge cap + --force-retry reset.
         'complete wins' preserved; no partial can regress a completed migration.
Bug 5  — v0.14.0 migration registered. src/commands/migrations/v0_14_0.ts
         ships Phase A (ALTER minion_jobs.max_stalled SET DEFAULT 3) + Phase B
         (pending-host-work ping for shell-jobs adoption).
Bug 6/10 — jsonb_agg(DISTINCT ...) in legacy traverseGraph (both engines).
         Presentation-level dedup; schema still preserves provenance rows.
Bug 7  — doctor --fast reads DB URL source via getDbUrlSource() in config.ts.
         Precise message: 'Skipping DB checks (--fast mode, URL present from env)'
         replaces the misleading 'No database configured'.
Bug 8  — max_stalled default bumped 1→3 in schema-embedded.ts, pglite-schema.ts,
         schema.sql (new installs). v0_14_0 Phase A ALTER for existing installs.
         autopilot-cycle handler yields to event loop between phases so the
         worker's lock-renewal timer fires on huge brains. (Deep AbortSignal
         threading through runEmbedCore/runExtractCore/runBacklinksCore/performSync
         deferred to v0.15 queue polish.)
Bug 9  — Gate sync.last_commit on no-failures across all three sync paths
         (incremental, full via runImport, gbrain import git continuity).
         recordSyncFailures() helper + ~/.gbrain/sync-failures.jsonl with
         dedup key path+commit+error-hash. New flags: --skip-failed (ack) +
         --retry-failed (re-attempt). Doctor surfaces unacknowledged failures.
Bug 11 — brain_score breakdown fields on BrainHealth (embed_coverage_score,
         link_density_score, timeline_coverage_score, no_orphans_score,
         no_dead_links_score); sum equals brain_score by construction.
         dead_links now on the type (resolves featuresTeaserForDoctor drift).
         orphan_pages kept as 'islanded' (no inbound AND no outbound) and
         docs updated to match — explicit semantic instead of doc drift.

New tests: test/traverse-graph-dedup.test.ts, test/sync-failures.test.ts,
test/brain-score-breakdown.test.ts, test/migration-resume.test.ts,
test/migrations-v0_14_0.test.ts. Extended: migrate, doctor, apply-migrations.

All 1696 unit tests pass locally. postgres-jsonb E2E regression unchanged
(none of these touch the JSONB write surface).

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

* docs: v0.14.2 CHANGELOG + CLAUDE.md; align migration-flow E2E with runner-owned ledger

CHANGELOG: v0.14.2 entry in the standard release-summary format
(two-line headline + lead + numbers table + "what this means" +
"To take advantage of v0.14.2" self-repair block + itemized
changes grouped by reliability / observability / graph correctness /
new migration / tests / deferred-to-v0.15).

CLAUDE.md: new "Key commands added in v0.14.2" section covers
--skip-failed, --retry-failed, --force-retry, GBRAIN_POOL_SIZE env,
and the new doctor checks (sync_failures, brain_score breakdown).
Migration orchestrator docs updated to describe v0_14_0.ts + the
runner-owned ledger contract from Bug 3.

test/e2e/migration-flow.test.ts: three assertions updated to match
the Bug 3 contract — orchestrators no longer append to completed.jsonl
directly, so direct-orchestrator E2E calls leave the ledger empty.
Preferences assertions remain (that's still the orchestrator's side
of the contract). Runner's ledger write is covered by the unit suite
(test/apply-migrations.test.ts + test/migration-resume.test.ts).

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

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

test/e2e/migration-flow.test.ts

@@ -121,13 +121,14 @@ describeE2E('E2E: v0.11.0 orchestrator against live Postgres', () => {
     expect(prefs.set_at).toBeTruthy();
     expect(prefs.set_in_version).toBeTruthy();
 
-    // Phase G: completed.jsonl has one entry for v0.11.0.
+    // Bug 3 (v0.14.2) — orchestrator no longer writes completed.jsonl.
+    // The runner (apply-migrations.ts) persists the result after the
+    // orchestrator returns. A direct orchestrator call in E2E leaves the
+    // ledger empty; the runner path is tested separately in
+    // test/apply-migrations.test.ts + test/migration-resume.test.ts.
     const completed = loadCompletedMigrations();
-    expect(completed.length).toBeGreaterThanOrEqual(1);
     const v0110Entries = completed.filter(e => e.version === '0.11.0');
-    expect(v0110Entries.length).toBe(1);
-    expect(['complete', 'partial']).toContain(v0110Entries[0].status!);
-    expect(v0110Entries[0].mode).toBe('pain_triggered');
+    expect(v0110Entries.length).toBe(0);
 
     // Phase F is skipped per COMMON_OPTS — autopilot should NOT have been
     // installed on this host.
@@ -142,15 +143,13 @@ describeE2E('E2E: v0.11.0 orchestrator against live Postgres', () => {
     const second = await v0_11_0.orchestrator(COMMON_OPTS);
     expect(['complete', 'partial']).toContain(second.status);
 
-    // completed.jsonl accumulates entries per run (each run appends one).
-    // The runtime semantics for resume are governed by the diff rule in
-    // apply-migrations; here we just assert the orchestrator itself doesn't
-    // blow up or produce different results on a second run.
-    const completed = loadCompletedMigrations();
-    const v0110 = completed.filter(e => e.version === '0.11.0');
-    expect(v0110.length).toBeGreaterThanOrEqual(2);
-    // Preferences should be stable (same mode, unchanged content).
+    // Bug 3 (v0.14.2) — orchestrator does not write completed.jsonl, so
+    // repeated direct invocations don't accumulate ledger entries. Assert
+    // the preferences state stays stable (the real idempotency signal for
+    // this orchestrator is "running again doesn't corrupt preferences").
     expect(loadPreferences().minion_mode).toBe('pain_triggered');
+    const completed = loadCompletedMigrations();
+    expect(completed.filter(e => e.version === '0.11.0').length).toBe(0);
   }, 90_000);
 
   test('host rewrite: builtin handlers auto-rewritten, non-builtins queued as JSONL TODOs', async () => {
@@ -233,15 +232,16 @@ describeE2E('E2E: v0.11.0 orchestrator against live Postgres', () => {
 
     // Orchestrator re-running on a partial → should succeed (schema apply
     // and smoke are idempotent; prefs are preserved from the partial
-    // record; host-rewrite runs its safe-skip pass; completed appends a
-    // new status:"complete" row).
+    // record; host-rewrite runs its safe-skip pass). Per Bug 3 (v0.14.2),
+    // the orchestrator itself doesn't append to completed.jsonl — the
+    // runner does. The stopgap's partial entry stays unchanged here.
     const result = await v0_11_0.orchestrator(COMMON_OPTS);
     expect(['complete', 'partial']).toContain(result.status);
 
     const completed = loadCompletedMigrations();
     const v0110 = completed.filter(e => e.version === '0.11.0');
-    // 1 partial (stopgap) + 1 post-orchestrator entry.
-    expect(v0110.length).toBe(2);
+    // Just the stopgap partial — orchestrator doesn't add its own entry.
+    expect(v0110.length).toBe(1);
     expect(v0110[0].status).toBe('partial');
     expect(v0110[0].source).toBe('fix-v0.11.0.sh');
   }, 90_000);