Resolves migration version collision: master shipped v58
(edges_backfilled_at_v0_33_3 — v0.33.3 W0c symbol-resolution backfill
watermark) ahead of this branch. The embed-perf cherry-pick from PR #987
also claimed v58 for its idx_chunks_embedding_null partial index;
renumbered to v59 since master landed first. Both migrations coexist
unchanged at their new slots.

No other conflicts. Typecheck clean.

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

Lands the 9 decisions + regression test set from /plan-eng-review on PR #991's
embed-perf cherry-pick. Implements the codex outside-voice findings folded in
during plan review.

Architecture / correctness:
- D2 jitter on the parsed retry-after delay (±30%) so 20 concurrent workers
  don't relock on the next 429 wave (thundering herd fix).
- D3 + D3a + D8 wall-clock budget (GBRAIN_EMBED_TIME_BUDGET_MS, default 30
  min) threaded as an AbortSignal into THREE places: the retry sleep
  (abortableSleep), the per-key worker claim loop, and the gateway embed
  call itself (so a worker mid-fetch on a ~30s OpenAI HTTP timeout cancels
  within seconds instead of waiting it out).
- D4 structured 429 detection that unwraps the gateway's AITransientError
  wrap via cause chain (depth-limited to 5). Naive `e.status === 429` was
  silently false against normalized errors; message-match stays as
  fallback. detect429FromCause exported as @internal helper.
- D4a `maxRetries: 0` passthrough through embedBatch → gateway →
  embedMany so the AI SDK's default 2-retry stack doesn't multiply this
  wrapper's 5 attempts (was up to 15 total cycles per call).
- D6 migration v59 (embed_stale_partial_index) rewritten to use
  CREATE INDEX CONCURRENTLY + handler-based engine-branching (mirrors v14
  invalid-remnant pattern). Plain CREATE INDEX would have taken ShareLock
  on the 373K-row content_chunks table for the duration of the build.
- D7 sourceId threaded through countStaleChunks + listStaleChunks +
  embedAllStale. `gbrain embed --stale --source X` was silently dropping
  the flag pre-fix and counting/embedding across every source. Both
  Postgres and PGLite engines updated.

Tests added:
- D5 8 unit cases for embedBatchWithBackoff in test/embed.serial.test.ts:
  ms / s retry-after parse, fallback, non-rate-limit rethrow, jitter
  variance, budget abort during sleep+fetch, normalized-error cause
  unwrap, maxRetries:0 passthrough verification.
- D5a fixed every pre-existing stale-row mock to include source_id +
  page_id (required on StaleChunkRow as of v0.33.3 cursor pagination —
  TypeScript's structural typing was hiding these).
- D7 unit cases asserting CLI `--source X` parses + threads sourceId.
- Gap scan: end-to-end wall-clock budget firing in the outer pagination
  loop via runEmbedCore.
- D6 migration v59 test cases in test/migrate.test.ts: source-shape
  assertion (CONCURRENTLY + invalid-remnant DROP-before-CREATE ordering),
  PGLite handler-branch idempotency, partial-index materialization.
- REGRESSION: new test/e2e/embed-stale-pagination.test.ts covering
  static (every chunk visited exactly once), failed-page (cursor advances
  past failures, next run picks up), page-split-across-batches,
  source-scoped scan, duplicate-slug-across-sources.
- PGLite parity cases for cursor pagination, page split, source filter
  in test/pglite-engine.test.ts (pins tuple-compare against WASM build).

Gate:
- bun run test: 6305 pass / 0 fail / 0 skip across all 8 shards + serial.
- DATABASE_URL=... bun run test:e2e: 90 files, 603 tests, 0 failures.

Plan: ~/.claude/plans/system-instruction-you-are-working-iterative-torvalds.md

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

Master shipped v0.34.0.0 Cathedral III which claimed migration v59
(code_traversal_cache_v0_34). The embed-perf branch's idx_chunks_embedding_null
was at v59 from the prior merge wave; renumbered to v60 since master
landed first. Both migrations coexist unchanged at their final slots.

Also fixed a TypeScript stricter-cast nit in the new E2E test (postgres.js
RowList -> typed array now requires going through unknown first; master
likely bumped TS or postgres.js types).

Full unit suite passes: 6385 / 0 / 0 across 8 shards + serial.
Full E2E suite passes against fresh Postgres: 90 files / 603 tests / 0 fail
(verified in the prior commit; re-running is gated on Docker availability).

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

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

Master shipped v0.34.3.0 (PR #1003, supervisor clean-exit watchdog fix).
No new migrations — only src/core/minions/* + src/commands/autopilot.ts
touched, so our v66 partial-index migration stays in place.

Conflict resolutions:
- VERSION: take 0.34.4.0
- package.json: take 0.34.4.0
- CHANGELOG.md: clean non-interleaved conflict; strip markers and keep
  both entries (v0.34.4.0 on top, v0.34.3.0 below, then the existing
  v0.34.2.0 and v0.34.1.0 in descending order)

Typecheck clean.

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