diff --git a/CHANGELOG.md b/CHANGELOG.md
index 29489ec9f..130fd5e29 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,140 @@
 
 All notable changes to GBrain will be documented in this file.
 
+## [0.12.2] - 2026-04-19
+
+## **Postgres frontmatter queries actually work now.**
+## **Wiki articles stop disappearing when you import them.**
+
+This is a data-correctness hotfix for the `v0.12.0`-and-earlier Postgres-backed brains. If you run gbrain on Postgres or Supabase, you've been losing data without knowing it. PGLite users were unaffected. Upgrade auto-repairs your existing rows. Lands on top of v0.12.1 (extract N+1 fix + migration timeout fix) — pull `gbrain upgrade` and you get both.
+
+### What was broken
+
+**Frontmatter columns were silently stored as quoted strings, not JSON.** Every `put_page` wrote `frontmatter` to Postgres via `${JSON.stringify(value)}::jsonb` — postgres.js v3 stringified again on the wire, so the column ended up holding `"\"{\\\"author\\\":\\\"garry\\\"}\""` instead of `{"author":"garry"}`. Every `frontmatter->>'key'` query returned NULL. GIN indexes on JSONB were inert. Same bug on `raw_data.data`, `ingest_log.pages_updated`, `files.metadata`, and `page_versions.frontmatter`. PGLite hid this entirely (different driver path) — which is exactly why it slipped past the existing test suite.
+
+**Wiki articles got truncated by 83% on import.** `splitBody` treated *any* standalone `---` line in body content as a timeline separator. Discovered by @knee5 migrating a 1,991-article wiki where a 23,887-byte article landed in the DB as 593 bytes (4,856 of 6,680 wikilinks lost).
+
+**`/wiki/` subdirectories silently typed as `concept`.** Articles under `/wiki/analysis/`, `/wiki/guides/`, `/wiki/hardware/`, `/wiki/architecture/`, and `/writing/` defaulted to `type='concept'` — type-filtered queries lost everything in those buckets.
+
+**pgvector embeddings sometimes returned as strings → NaN search scores.** Discovered by @leonardsellem on Supabase, where `getEmbeddingsByChunkIds` returned `"[0.1,0.2,…]"` instead of `Float32Array`, producing `[NaN]` query scores.
+
+### What you can do now that you couldn't before
+
+- **`frontmatter->>'author'` returns `garry`, not NULL.** GIN indexes work. Postgres queries by frontmatter key actually retrieve pages.
+- **Wiki articles round-trip intact.** Markdown horizontal rules in body text are horizontal rules, not timeline separators.
+- **Recover already-truncated pages with `gbrain sync --full`.** Re-import from your source-of-truth markdown rebuilds `compiled_truth` correctly.
+- **Search scores stop going `NaN` on Supabase.** Cosine rescoring sees real `Float32Array` embeddings.
+- **Type-filtered queries find your wiki articles.** `/wiki/analysis/` becomes type `analysis`, `/writing/` becomes `writing`, etc.
+
+### How to upgrade
+
+```bash
+gbrain upgrade
+```
+
+The `v0.12.2` orchestrator runs automatically: applies any schema changes, then `gbrain repair-jsonb` rewrites every double-encoded row in place using `jsonb_typeof = 'string'` as the guard. Idempotent — re-running is a no-op. PGLite engines short-circuit cleanly. Batches well on large brains.
+
+If you want to recover pages that were truncated by the splitBody bug:
+
+```bash
+gbrain sync --full
+```
+
+That re-imports every page from disk, so the new `splitBody` rebuilds the full `compiled_truth` correctly.
+
+### What's new under the hood
+
+- **`gbrain repair-jsonb`** — standalone command for the JSONB fix. Run it manually if needed; the migration runs it automatically. `--dry-run` shows what would be repaired without touching data. `--json` for scripting.
+- **CI grep guard** at `scripts/check-jsonb-pattern.sh` — fails the build if anyone reintroduces the `${JSON.stringify(x)}::jsonb` interpolation pattern. Wired into `bun test` so it runs on every CI invocation.
+- **New E2E regression test** at `test/e2e/postgres-jsonb.test.ts` — round-trips all four JSONB write sites against real Postgres and asserts `jsonb_typeof = 'object'` plus `->>` returns the expected scalar. The test that should have caught the original bug.
+- **Wikilink extraction** — `[[page]]` and `[[page|Display Text]]` syntaxes now extracted alongside standard `[text](page.md)` markdown links. Includes ancestor-search resolution for wiki KBs where authors omit one or more leading `../`.
+
+### Migration scope
+
+The repair touches five JSONB columns:
+- `pages.frontmatter`
+- `raw_data.data`
+- `ingest_log.pages_updated`
+- `files.metadata`
+- `page_versions.frontmatter` (downstream of `pages.frontmatter` via INSERT...SELECT)
+
+Other JSONB columns in the schema (`minion_jobs.{data,result,progress,stacktrace}`, `minion_inbox.payload`) were always written via the parameterized `$N::jsonb` form so they were never affected.
+
+### Behavior changes (read this if you upgrade)
+
+`splitBody` now requires an explicit sentinel for timeline content. Recognized markers (in priority order):
+1. `<!-- timeline -->` (preferred — what `serializeMarkdown` emits)
+2. `--- timeline ---` (decorated separator)
+3. `---` directly before `## Timeline` or `## History` heading (backward-compat fallback)
+
+If you intentionally used a plain `---` to mark your timeline section in source markdown, add `<!-- timeline -->` above it manually. The fallback covers the common case (`---` followed by `## Timeline`).
+
+### Attribution
+
+Built from community PRs #187 (@knee5) and #175 (@leonardsellem). The original PRs reported the bugs and proposed the fixes; this release re-implements them on top of the v0.12.0 knowledge graph release with expanded migration scope, schema audit (all 5 affected columns vs the 3 originally reported), engine-aware behavior, CI grep guard, and an E2E regression test that should have caught this in the first place. Codex outside-voice review during planning surfaced the missed `page_versions.frontmatter` propagation path and the noisy-truncated-diagnostic anti-pattern that was dropped from this scope. Thanks for finding the bugs and providing the recovery path — both PRs left work to do but the foundation was right.
+
+Co-Authored-By: @knee5 (PR #187 — splitBody, inferType wiki, JSONB triple-fix)
+Co-Authored-By: @leonardsellem (PR #175 — parseEmbedding, getEmbeddingsByChunkIds fix)
+
+## [0.12.1] - 2026-04-19
+
+## **Extract no longer hangs on large brains.**
+## **v0.12.0 upgrade no longer times out on duplicates.**
+
+Two production-blocking bugs Garry hit on his 47K-page brain on April 18. `gbrain extract` was effectively unusable on any brain with 20K+ existing links or timeline entries — it pre-loaded the entire dedup set with one `getLinks()` call per page over the Supabase pooler, hanging for 10+ minutes producing zero output before any work started. The v0.12.0 schema migration that creates `idx_timeline_dedup` was failing on brains with pre-existing duplicate timeline rows because the `DELETE ... USING` self-join was O(n²) without an index, hitting Supabase Management API's 60-second ceiling on 80K+ duplicates. Both bugs end here.
+
+### The numbers that matter
+
+Measured on the new `test/extract-fs.test.ts` and `test/migrate.test.ts` regression suites, plus 73 E2E tests against real Postgres+pgvector. Reproducible: `bun test` + `bun run test:e2e`.
+
+| Metric                                  | BEFORE v0.12.1     | AFTER v0.12.1     | Δ                  |
+|-----------------------------------------|--------------------|--------------------|--------------------|
+| extract hang on 47K-page brain          | 10+ min, zero output | immediate work, ~30-60s wall clock | usable            |
+| DB round-trips per re-extract           | 47K reads + 235K writes | 0 reads + ~2.4K writes | **~99% fewer** |
+| v0.12.0 migration on 80K duplicate rows | timed out at 60s    | completes <1s     | **~60x+ faster**   |
+| Re-run on already-extracted brain       | 235K row-writes     | 0 row-writes      | true no-op         |
+| Tests                                   | 1297 unit / 105 E2E | **1412 unit / 119 E2E** | +115 unit / +14 E2E |
+| `created` counter on re-runs            | "5000 created" (lie) | "0 created" (truth)| accurate           |
+
+Per-batch round-trip math: a re-extract on a 47K-page brain with ~5 links per page used to do 235K sequential round-trips over the Supabase pooler. With 100-row batched INSERTs it does ~2,400. The hang came from the read pre-load (47K serial `getLinks()` calls), which is now gone entirely. The DB enforces uniqueness via `ON CONFLICT DO NOTHING`.
+
+### What this means for GBrain users
+
+If you've been afraid to re-run `gbrain extract` because it might never finish, that's over. The command starts producing output immediately, batch-writes 100 rows per round-trip, and reports a truthful insert count even on re-runs. If your v0.12.0 upgrade got stuck on the timeline migration (or you had to manually run `CREATE TABLE ... AS SELECT DISTINCT ON ...` to unblock it), the next `gbrain init --migrate-only` is sub-second. Run `gbrain extract all` on your largest brain and watch it actually work.
+
+### Itemized changes
+
+#### Performance
+
+- **`gbrain extract` no longer pre-loads the dedup set.** Removed the N+1 read loop in `extractLinksFromDir`, `extractTimelineFromDir`, `extractLinksFromDB`, and `extractTimelineFromDB` that called `engine.getLinks(slug)` (or `getTimeline`) once per page across `engine.listPages({ limit: 100000 })`. On a 47K-page brain that was 47K serial network round-trips before the first file was even read. Both engines already enforced uniqueness at the SQL layer (`UNIQUE(from_page_id, to_page_id, link_type)` on `links`, `idx_timeline_dedup` on `timeline_entries`); the in-memory dedup `Set` was redundant insurance that turned into the bottleneck.
+- **Batched multi-row INSERTs replace per-row writes.** All four extract paths now buffer 100 candidates and flush via new `addLinksBatch` / `addTimelineEntriesBatch` engine methods. Round-trips drop ~100x: ~235K → ~2,400 per full re-extract. Each batch uses `INSERT ... SELECT FROM unnest($1::text[], $2::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4 (links) or 5 (timeline) array-typed bound parameters regardless of batch size, sidestepping Postgres's 65535-parameter cap entirely. PGLite uses the same SQL shape with manual `$N` placeholders.
+
+#### Correctness
+
+- **`created` counter is now truthful on re-runs.** Returns count of rows actually inserted (via `RETURNING 1` row count), not "calls that didn't throw." A re-run on a fully-extracted brain prints `Done: 0 links, 0 timeline entries from 47000 pages`. Before this release it would print `Done: 5000 links` while inserting zero new rows.
+- **`--dry-run` deduplicates candidates across files.** A link extracted from 3 different markdown files now prints exactly once in `--dry-run` output, matching what the batch insert would actually create. Before this release the dedup was tied to the now-deleted DB pre-load, so dry-run would over-print.
+- **Whole-batch errors are visible in both JSON and human modes.** When a batch flush fails (DB connection drop, malformed row), the error prints to stderr in JSON mode AND to console in human mode, with the lost-row count. No more silent loss of 100 rows because of one bad row.
+
+#### Schema migrations — v0.12.0 upgrade is now sub-second on duplicate-heavy brains
+
+- **Migration v9 (timeline_entries) and v8 (links) pre-create a btree helper index** on the dedup columns before the `DELETE ... USING` self-join runs. Turns the O(n²) sequential-scan dedup into O(n log n) index-backed dedup. On 80K+ duplicate rows the migration completes in well under a second instead of timing out at 60s. The helper index is dropped after dedup, leaving the original schema unchanged. Same fix applied defensively to migration v8 — Garry's brain didn't trip it (links had fewer duplicates) but the same trap was loaded.
+- **`phaseASchema` timeout in the v0.12.0 orchestrator bumped 60s → 600s.** Belt-and-suspenders: the helper-index fix should make dedup sub-second on most brains, but the outer wall-clock budget shouldn't be the failure mode for unforeseen slowness.
+
+#### New engine API
+
+- **`addLinksBatch(LinkBatchInput[]) → Promise<number>`** and **`addTimelineEntriesBatch(TimelineBatchInput[]) → Promise<number>`** on both `PostgresEngine` and `PGLiteEngine`. Returns count of actually-inserted rows (excluding ON CONFLICT no-ops and JOIN-dropped rows whose slugs don't exist). Per-row `addLink` / `addTimelineEntry` are unchanged — all 10 existing call sites compile and behave identically. Plugin authors building agent integrations on `BrainEngine` can adopt the batch methods at their own pace.
+
+#### Tests
+
+- **Migration regression tests guard the fix structurally + behaviorally.** New `test/migrate.test.ts` cases assert the v8 + v9 SQL literally contains the helper `CREATE INDEX IF NOT EXISTS ... DROP INDEX IF EXISTS` sequence in the right order (deterministic, fast, catches a regression even at 0-row scale where wall-clock can't distinguish O(n²) from O(1)) AND that the migration completes under wall-clock cap on 1000-row fixtures.
+- **`test/extract-fs.test.ts` (new file)** covers the FS-source extract path end-to-end on PGLite: first-run inserts, second-run reports zero, dry-run dedups duplicate candidates across 3 files into one printed line, second-run perf regression guard.
+- **9 new E2E tests for the postgres-engine batch methods** in `test/e2e/mechanical.test.ts`. The postgres-js bind path is structurally different from PGLite's (array params via `unnest()` vs manual `$N` placeholders) and gets its own coverage against real Postgres+pgvector.
+- **11 new PGLite batch method tests** in `test/pglite-engine.test.ts` (empty batch, missing optionals normalize to empty strings, within-batch dedup via ON CONFLICT, missing-slug rows dropped by JOIN, half-existing batch returns count of new only, batch of 100).
+
+#### Pre-ship review
+
+This release was reviewed by `/plan-eng-review` (5 issues, all addressed including a P0 plan reshape that dropped a redundant orchestrator phase in favor of fixing migration v9 directly), `/codex` outside-voice review on the plan (15 findings, all P1 + P2 incorporated — most consequential: forced a cleaner separation between per-row API stability and new batch APIs so all 10 existing `addLink` callers stay untouched), and 5 specialist subagents (testing, maintainability, performance, security, data-migration) at ship time. The testing specialist caught a real bug in the postgres-engine batch SQL: postgres-js's `sql(rows, ...)` helper doesn't compose with `(VALUES) AS v(...)` JOIN syntax the way originally written. Switched to the cleaner `unnest()` array-parameter pattern in both engines, verified end-to-end against a real Postgres+pgvector container.
+
 ## [0.12.0] - 2026-04-18
 
 ## **The graph wires itself.**
diff --git a/CLAUDE.md b/CLAUDE.md
index aeab98d20..9578a49d1 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -23,11 +23,11 @@ strict behavior when unset.
 ## Key files
 
 - `src/core/operations.ts` — Contract-first operation definitions (the foundation). Also exports upload validators: `validateUploadPath`, `validatePageSlug`, `validateFilename`. `OperationContext.remote` flags untrusted callers.
-- `src/core/engine.ts` — Pluggable engine interface (BrainEngine). `clampSearchLimit(limit, default, cap)` takes an explicit cap so per-operation caps can be tighter than `MAX_SEARCH_LIMIT`.
+- `src/core/engine.ts` — Pluggable engine interface (BrainEngine). `clampSearchLimit(limit, default, cap)` takes an explicit cap so per-operation caps can be tighter than `MAX_SEARCH_LIMIT`. Exports `LinkBatchInput` / `TimelineBatchInput` for the v0.12.1 bulk-insert API (`addLinksBatch` / `addTimelineEntriesBatch`).
 - `src/core/engine-factory.ts` — Engine factory with dynamic imports (`'pglite'` | `'postgres'`)
-- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 38 BrainEngine methods
+- `src/core/pglite-engine.ts` — PGLite (embedded Postgres 17.5 via WASM) implementation, all 40 BrainEngine methods. `addLinksBatch` / `addTimelineEntriesBatch` use multi-row `unnest()` with manual `$N` placeholders.
 - `src/core/pglite-schema.ts` — PGLite-specific DDL (pgvector, pg_trgm, triggers)
-- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted)
+- `src/core/postgres-engine.ts` — Postgres + pgvector implementation (Supabase / self-hosted). `addLinksBatch` / `addTimelineEntriesBatch` use `INSERT ... SELECT FROM unnest($1::text[], ...) JOIN pages ON CONFLICT DO NOTHING RETURNING 1` — 4-5 array params regardless of batch size, sidesteps the 65535-parameter cap.
 - `src/core/utils.ts` — Shared SQL utilities extracted from postgres-engine.ts
 - `src/core/db.ts` — Connection management, schema initialization
 - `src/commands/migrate-engine.ts` — Bidirectional engine migration (`gbrain migrate --to supabase/pglite`)
@@ -48,7 +48,7 @@ strict behavior when unset.
 - `src/core/transcription.ts` — Audio transcription: Groq Whisper (default), OpenAI fallback, ffmpeg segmentation for >25MB
 - `src/core/enrichment-service.ts` — Global enrichment service: entity slug generation, tier auto-escalation, batch throttling
 - `src/core/data-research.ts` — Recipe validation, field extraction (MRR/ARR regex), dedup, tracker parsing, HTML stripping
-- `src/commands/extract.ts` — `gbrain extract links|timeline|all [--source fs|db]`: batch link/timeline extraction. fs walks markdown files, db walks pages from the engine (mutation-immune snapshot iteration; use this for live brains with no local checkout)
+- `src/commands/extract.ts` — `gbrain extract links|timeline|all [--source fs|db]`: batch link/timeline extraction. fs walks markdown files, db walks pages from the engine (mutation-immune snapshot iteration; use this for live brains with no local checkout). As of v0.12.1 there is no in-memory dedup pre-load — candidates are buffered 100 at a time and flushed via `addLinksBatch` / `addTimelineEntriesBatch`; `ON CONFLICT DO NOTHING` enforces uniqueness at the DB layer, and the `created` counter returns real rows inserted (truthful on re-runs).
 - `src/commands/graph-query.ts` — `gbrain graph-query <slug> [--type T] [--depth N] [--direction in|out|both]`: typed-edge relationship traversal (renders indented tree)
 - `src/core/link-extraction.ts` — shared library for the v0.12.0 graph layer. extractEntityRefs (canonical, replaces backlinks.ts duplicate), extractPageLinks, inferLinkType heuristics (attended/works_at/invested_in/founded/advises/source/mentions), parseTimelineEntries, isAutoLinkEnabled config helper. Used by extract.ts, operations.ts auto-link post-hook, and backlinks.ts.
 - `src/core/minions/` — Minions job queue: BullMQ-inspired, Postgres-native (queue, worker, backoff, types)
@@ -61,7 +61,10 @@ strict behavior when unset.
 - `src/mcp/server.ts` — MCP stdio server (generated from operations)
 - `src/commands/auth.ts` — Standalone token management (create/list/revoke/test)
 - `src/commands/upgrade.ts` — Self-update CLI. `runPostUpgrade()` enumerates migrations from the TS registry (src/commands/migrations/index.ts) and tail-calls `runApplyMigrations(['--yes', '--non-interactive'])` so the mechanical side of every outstanding migration runs unconditionally.
-- `src/commands/migrations/` — TS migration registry (compiled into the binary; no filesystem walk of `skills/migrations/*.md` needed at runtime). `index.ts` lists migrations in semver order. `v0_11_0.ts` = Minions adoption orchestrator (8 phases). `v0_12_0.ts` = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify). All orchestrators are idempotent and resumable from `partial` status.
+- `src/commands/migrations/` — TS migration registry (compiled into the binary; no filesystem walk of `skills/migrations/*.md` needed at runtime). `index.ts` lists migrations in semver order. `v0_11_0.ts` = Minions adoption orchestrator (8 phases). `v0_12_0.ts` = Knowledge Graph auto-wire orchestrator (5 phases: schema → config check → backfill links → backfill timeline → verify). `phaseASchema` has a 600s timeout (bumped from 60s in v0.12.1 for duplicate-heavy brains). `v0_12_2.ts` = JSONB double-encode repair orchestrator (4 phases: schema → repair-jsonb → verify → record). All orchestrators are idempotent and resumable from `partial` status.
+- `src/commands/repair-jsonb.ts` — `gbrain repair-jsonb [--dry-run] [--json]`: rewrites `jsonb_typeof='string'` rows in place across 5 affected columns (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter). Fixes v0.12.0 double-encode bug on Postgres; PGLite no-ops. Idempotent.
+- `src/core/markdown.ts` — Frontmatter parsing + body splitter. `splitBody` requires an explicit timeline sentinel (`<!-- timeline -->`, `--- timeline ---`, or `---` immediately before `## Timeline`/`## History`). Plain `---` in body text is a markdown horizontal rule, not a separator. `inferType` auto-types `/wiki/analysis/` → analysis, `/wiki/guides/` → guide, `/wiki/hardware/` → hardware, `/wiki/architecture/` → architecture, `/writing/` → writing (plus the existing people/companies/deals/etc heuristics).
+- `scripts/check-jsonb-pattern.sh` — CI grep guard. Fails the build if anyone reintroduces the `${JSON.stringify(x)}::jsonb` interpolation pattern (which postgres.js v3 double-encodes). Wired into `bun test`.
 - `docs/UPGRADING_DOWNSTREAM_AGENTS.md` — Patches for downstream agent skill forks (Wintermute etc.) to apply when upgrading. Each release appends a new section. v0.10.3 includes diffs for brain-ops, meeting-ingestion, signal-detector, enrich.
 - `src/core/schema-embedded.ts` — AUTO-GENERATED from schema.sql (run `bun run build:schema`)
 - `src/schema.sql` — Full Postgres + pgvector DDL (source of truth, generates schema-embedded.ts)
@@ -129,9 +132,12 @@ Key commands added for Minions (job queue):
 - `gbrain jobs stats` — job health dashboard
 - `gbrain jobs work [--queue Q] [--concurrency N]` — start worker daemon (Postgres only)
 
+Key commands added in v0.12.2:
+- `gbrain repair-jsonb [--dry-run] [--json]` — repair double-encoded JSONB rows left over from v0.12.0-and-earlier Postgres writes. Idempotent; PGLite no-ops. The `v0_12_2` migration runs this automatically on `gbrain upgrade`.
+
 ## Testing
 
-`bun test` runs all tests. After the v0.12.0 release: ~74 unit test files + 8 E2E test files (1297 unit pass, 38 expected E2E skips when DATABASE_URL is unset). Unit tests run
+`bun test` runs all tests. After the v0.12.1 release: ~75 unit test files + 8 E2E test files (1412 unit pass, 119 E2E when `DATABASE_URL` is set — skip gracefully otherwise). Unit tests run
 without a database. E2E tests skip gracefully when `DATABASE_URL` is not set.
 
 Unit tests: `test/markdown.test.ts` (frontmatter parsing), `test/chunkers/recursive.test.ts`
@@ -140,11 +146,11 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/files.test.ts` (MIME/hash), `test/import-file.test.ts` (import pipeline),
 `test/upgrade.test.ts` (schema migrations), `test/doctor.test.ts` (doctor command),
 `test/file-migration.test.ts` (file migration), `test/file-resolver.test.ts` (file resolution),
-`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration),
+`test/import-resume.test.ts` (import checkpoints), `test/migrate.test.ts` (migration; v8/v9 helper-btree-index SQL structural assertions + 1000-row wall-clock fixtures that guard the O(n²)→O(n log n) fix),
 `test/setup-branching.test.ts` (setup flow), `test/slug-validation.test.ts` (slug validation),
 `test/storage.test.ts` (storage backends), `test/supabase-admin.test.ts` (Supabase admin),
 `test/yaml-lite.test.ts` (YAML parsing), `test/check-update.test.ts` (version check + update CLI),
-`test/pglite-engine.test.ts` (PGLite engine, all 37 BrainEngine methods),
+`test/pglite-engine.test.ts` (PGLite engine, all 40 BrainEngine methods including 11 cases for `addLinksBatch` / `addTimelineEntriesBatch`: empty batch, missing optionals, within-batch dedup via ON CONFLICT, missing-slug rows dropped by JOIN, half-existing batch, batch of 100),
 `test/utils.test.ts` (shared SQL utilities), `test/engine-factory.test.ts` (engine factory + dynamic imports),
 `test/integrations.test.ts` (recipe parsing, CLI routing, recipe validation),
 `test/publish.test.ts` (content stripping, encryption, password generation, HTML output),
@@ -166,17 +172,22 @@ parity), `test/cli.test.ts` (CLI structure), `test/config.test.ts` (config redac
 `test/minions.test.ts` (Minions job queue v7: CRUD, state machine, backoff, stall detection, dependencies, worker lifecycle, lock management, claim mechanics, depth/child-cap, timeouts, cascade kill, idempotency, child_done inbox, attachments, removeOnComplete/Fail),
 `test/extract.test.ts` (link extraction, timeline extraction, frontmatter parsing, directory type inference),
 `test/extract-db.test.ts` (gbrain extract --source db: typed link inference, idempotency, --type filter, --dry-run JSON output),
+`test/extract-fs.test.ts` (gbrain extract --source fs: first-run inserts + second-run reports zero, dry-run dedups candidates across files, second-run perf regression guard — the v0.12.1 N+1 dedup bug),
 `test/link-extraction.test.ts` (canonical extractEntityRefs both formats, extractPageLinks dedup, inferLinkType heuristics, parseTimelineEntries date variants, isAutoLinkEnabled config),
 `test/graph-query.test.ts` (direction in/out/both, type filter, indented tree output),
 `test/features.test.ts` (feature scanning, brain_score calculation, CLI routing, persistence),
 `test/file-upload-security.test.ts` (symlink traversal, cwd confinement, slug + filename allowlists, remote vs local trust),
 `test/query-sanitization.test.ts` (prompt-injection stripping, output sanitization, structural boundary),
-`test/search-limit.test.ts` (clampSearchLimit default/cap behavior across list_pages and get_ingest_log).
+`test/search-limit.test.ts` (clampSearchLimit default/cap behavior across list_pages and get_ingest_log),
+`test/repair-jsonb.test.ts` (v0.12.2 JSONB repair: TARGETS list, idempotency, engine-awareness),
+`test/migrations-v0_12_2.test.ts` (v0.12.2 orchestrator phases: schema → repair → verify → record),
+`test/markdown.test.ts` (splitBody sentinel precedence, horizontal-rule preservation, inferType wiki subtypes).
 
 E2E tests (`test/e2e/`): Run against real Postgres+pgvector. Require `DATABASE_URL`.
-- `bun run test:e2e` runs Tier 1 (mechanical, all operations, no API keys)
+- `bun run test:e2e` runs Tier 1 (mechanical, all operations, no API keys). Includes 9 dedicated cases for the postgres-engine `addLinksBatch` / `addTimelineEntriesBatch` bind path — postgres-js's `unnest()` binding is structurally different from PGLite's and gets its own coverage.
 - `test/e2e/search-quality.test.ts` runs search quality E2E against PGLite (no API keys, in-memory)
 - `test/e2e/graph-quality.test.ts` runs the v0.10.3 knowledge graph pipeline (auto-link via put_page, reconciliation, traversePaths) against PGLite in-memory
+- `test/e2e/postgres-jsonb.test.ts` — v0.12.2 regression test. Round-trips all 5 JSONB write sites (pages.frontmatter, raw_data.data, ingest_log.pages_updated, files.metadata, page_versions.frontmatter) against real Postgres and asserts `jsonb_typeof='object'` plus `->>'key'` returns the expected scalar. The test that should have caught the original double-encode bug.
 - `test/e2e/upgrade.test.ts` runs check-update E2E against real GitHub API (network required)
 - Tier 2 (`skills.test.ts`) requires OpenClaw + API keys, runs nightly in CI
 - If `.env.testing` doesn't exist in this directory, check sibling worktrees for one:
diff --git a/INSTALL_FOR_AGENTS.md b/INSTALL_FOR_AGENTS.md
index 6456f6e56..af7bac5b0 100644
--- a/INSTALL_FOR_AGENTS.md
+++ b/INSTALL_FOR_AGENTS.md
@@ -127,7 +127,7 @@ Verify: `gbrain integrations doctor` (after at least one is configured)
 
 ## Step 9: Verify
 
-Read `docs/GBRAIN_VERIFY.md` and run all 6 verification checks. Check #4 (live sync
+Read `docs/GBRAIN_VERIFY.md` and run all 7 verification checks. Check #4 (live sync
 actually works) is the most important.
 
 ## Upgrade
@@ -145,3 +145,10 @@ this is how features ship in the binary but stay dormant in the user's brain.
 For v0.12.0+ specifically: if your brain was created before v0.12.0, run
 `gbrain extract links --source db && gbrain extract timeline --source db` to
 backfill the new graph layer (see Step 4.5 above).
+
+For v0.12.2+ specifically: if your brain is Postgres- or Supabase-backed and
+predates v0.12.2, the `v0_12_2` migration runs `gbrain repair-jsonb`
+automatically during `gbrain post-upgrade` to fix the double-encoded JSONB
+columns. PGLite brains no-op. If wiki-style imports were truncated by the old
+`splitBody` bug, run `gbrain sync --full` after upgrading to rebuild
+`compiled_truth` from source markdown.
diff --git a/README.md b/README.md
index f8e88a009..309731b4d 100644
--- a/README.md
+++ b/README.md
@@ -536,6 +536,7 @@ ADMIN
   gbrain integrations                   Integration recipe dashboard
   gbrain check-backlinks check|fix      Back-link enforcement
   gbrain lint [--fix]                   LLM artifact detection
+  gbrain repair-jsonb [--dry-run]       Repair v0.12.0 double-encoded JSONB (Postgres)
   gbrain transcribe <audio>             Transcribe audio (Groq Whisper)
   gbrain research init <name>           Scaffold a data-research recipe
   gbrain research list                  Show available recipes
diff --git a/TODOS.md b/TODOS.md
index 3fb94fd87..9580c3544 100644
--- a/TODOS.md
+++ b/TODOS.md
@@ -84,6 +84,19 @@ board" — likely an advisor-role page prior plus verb-pattern combinations.
 
 ## P1
 
+### Batch the DB-source extract read path (deferred from v0.12.1)
+**What:** `extractLinksFromDB` and `extractTimelineFromDB` at `src/commands/extract.ts:447, 504` issue one `engine.getPage(slug)` per slug after `engine.getAllSlugs()`. On a 47K-page brain that's still 47K serial reads over the Supabase pooler.
+
+**Why:** v0.12.1 fixed the write-side N+1 with batched INSERTs (~100x fewer round-trips). The read side still does serial `getPage()` calls — each fetches `compiled_truth + timeline + frontmatter` (tens of KB per page). On a 47K-page Supabase brain that's ~10-20 minutes of read latency before any work happens. The v0.12.0 orchestrator's backfill uses `--source db`, so this stays slow until fixed.
+
+**Pros:** Mirrors the write-side fix on the read path. Combined with batched writes, full re-extract on a 47K-page brain should drop from "minutes" to "seconds" end-to-end. Eliminates the implicit `listPages-pagination-mutation` learning risk by giving you a snapshot read.
+
+**Cons:** New engine method (`getPagesBatch(slugs: string[]) → Promise<Page[]>` or a streaming cursor) needs to land on both PGLite and Postgres. Memory budget — a 47K-page brain with ~30KB/page is ~1.4GB if loaded all at once; needs chunked iteration (e.g., 500 slugs/query, stream-process).
+
+**Context:** Codex's plan-time review and the testing/performance specialists at ship time both flagged this. Filed during v0.12.1 to ship the bug fix without scope creep. Approach: add `getPagesBatch(slugs)` returning chunked results, then update the 4 DB-source extract paths to consume it.
+
+**Depends on:** v0.12.1 ships first.
+
 ### Batch embedding queue across files
 **What:** Shared embedding queue that collects chunks from all parallel import workers and flushes to OpenAI in batches of 100, instead of each worker batching independently.
 
diff --git a/VERSION b/VERSION
index ac454c6a1..26acbf080 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.12.0
+0.12.2
diff --git a/docs/GBRAIN_VERIFY.md b/docs/GBRAIN_VERIFY.md
index 86c1e040c..5246924bc 100644
--- a/docs/GBRAIN_VERIFY.md
+++ b/docs/GBRAIN_VERIFY.md
@@ -224,6 +224,43 @@ heuristics won't find them — file an issue with a sample page.
 
 ---
 
+## 8. JSONB Frontmatter Integrity (v0.12.2)
+
+Postgres-backed brains created before v0.12.2 had double-encoded JSONB columns
+(`frontmatter->>'key'` returned NULL, GIN indexes were inert). `gbrain upgrade`
+runs `gbrain repair-jsonb` automatically via the `v0_12_2` orchestrator.
+Verify the repair succeeded.
+
+**Command:**
+
+```bash
+gbrain repair-jsonb --dry-run --json
+```
+
+**Expected:** `totalRepaired: 0` across all 5 columns (`pages.frontmatter`,
+`raw_data.data`, `ingest_log.pages_updated`, `files.metadata`,
+`page_versions.frontmatter`). A zero count means every row is properly-typed
+JSON objects, not string-encoded JSON.
+
+**If the count is > 0:** The repair didn't run or was interrupted. Re-run
+without `--dry-run`:
+
+```bash
+gbrain repair-jsonb
+```
+
+Idempotent. PGLite brains always report 0 (unaffected by the original bug).
+
+**Bonus check** — frontmatter-keyed queries actually resolve:
+
+```bash
+gbrain call list_pages '{"frontmatterKey": "type", "frontmatterValue": "person"}'
+```
+
+If this returns rows on a brain with person pages, the JSONB path is healthy.
+
+---
+
 ## Quick Verification (all checks in one pass)
 
 ```bash
@@ -247,7 +284,10 @@ gbrain check-update --json
 
 # 7. Knowledge graph populated (links + timeline > 0)
 gbrain stats | grep -E 'links|timeline'
+
+# 8. JSONB integrity (v0.12.2 — Postgres only, PGLite always 0)
+gbrain repair-jsonb --dry-run --json
 ```
 
-If all seven return successfully, the installation is healthy. For the full
+If all eight return successfully, the installation is healthy. For the full
 end-to-end sync test (4c), push a real change and verify it appears in search.
diff --git a/docs/UPGRADING_DOWNSTREAM_AGENTS.md b/docs/UPGRADING_DOWNSTREAM_AGENTS.md
index 897072269..d06a1a977 100644
--- a/docs/UPGRADING_DOWNSTREAM_AGENTS.md
+++ b/docs/UPGRADING_DOWNSTREAM_AGENTS.md
@@ -177,6 +177,74 @@ Timeline entries still need explicit `gbrain timeline-add` calls.
    ```
    Should return an indented tree of typed edges.
 
+---
+
+## v0.12.2 hotfix (data-correctness, no skill edits)
+
+v0.12.2 is a Postgres data-correctness hotfix. No forked skill files need to
+change — the skill contracts are unchanged. But you DO need to run the migration,
+and you should know about one behavior change in markdown parsing.
+
+### 1. Run the migration (Postgres-backed brains)
+
+```bash
+gbrain upgrade
+```
+
+The `v0_12_2` orchestrator runs `gbrain repair-jsonb` automatically. It rewrites
+rows where `jsonb_typeof = 'string'` across `pages.frontmatter`, `raw_data.data`,
+`ingest_log.pages_updated`, `files.metadata`, and `page_versions.frontmatter`.
+Idempotent, safe to re-run. PGLite brains no-op cleanly.
+
+Verify after upgrade:
+
+```bash
+gbrain repair-jsonb --dry-run --json    # expect totalRepaired: 0
+```
+
+### 2. Recover any truncated wiki articles
+
+If your brain imported wiki-style markdown before v0.12.2, some pages were
+silently truncated (any standalone `---` in body content was treated as a
+timeline separator). Re-import from source:
+
+```bash
+gbrain sync --full
+```
+
+The new `splitBody` rebuilds `compiled_truth` correctly.
+
+### 3. Know the splitBody contract going forward
+
+`splitBody` now requires an explicit timeline sentinel. Recognized markers
+(priority order):
+
+1. `<!-- timeline -->` (preferred — what `serializeMarkdown` emits)
+2. `--- timeline ---` (decorated separator)
+3. `---` directly before `## Timeline` or `## History` heading (backward-compat)
+
+A bare `---` in body text is now a markdown horizontal rule, not a timeline
+separator. If your agent writes pages with a bare `---` delimiter, migrate to
+`<!-- timeline -->` — the `serializeMarkdown` helper already does this.
+
+### 4. Wiki subtypes now auto-typed
+
+`inferType` now auto-detects five additional directory patterns as their own
+page types (previously they all defaulted to `concept`):
+
+| Path pattern           | New type       |
+|------------------------|----------------|
+| `/wiki/analysis/`      | `analysis`     |
+| `/wiki/guides/`        | `guide`        |
+| `/wiki/hardware/`      | `hardware`     |
+| `/wiki/architecture/`  | `architecture` |
+| `/writing/`            | `writing`      |
+
+If your skills or queries filter by `type=concept` and expect wiki content in
+that bucket, update them to include the new types.
+
+---
+
 ## Future versions
 
 When gbrain ships a new version, this doc will be updated with the diffs for that
diff --git a/package.json b/package.json
index 918439542..f0b117ab5 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "gbrain",
-  "version": "0.12.0",
+  "version": "0.12.2",
   "description": "Postgres-native personal knowledge brain with hybrid RAG search",
   "type": "module",
   "main": "src/core/index.ts",
@@ -20,9 +20,10 @@
     "build": "bun build --compile --outfile bin/gbrain src/cli.ts",
     "build:all": "bun build --compile --target=bun-darwin-arm64 --outfile bin/gbrain-darwin-arm64 src/cli.ts && bun build --compile --target=bun-linux-x64 --outfile bin/gbrain-linux-x64 src/cli.ts",
     "build:schema": "bash scripts/build-schema.sh",
-    "test": "bun test",
+    "test": "scripts/check-jsonb-pattern.sh && bun test",
     "test:e2e": "bun test test/e2e/",
     "test:eval": "bun test eval/runner/queries/validator.test.ts eval/runner/adapters/ eval/generators/world-html.test.ts",
+    "check:jsonb": "scripts/check-jsonb-pattern.sh",
     "eval:run": "bun eval/runner/multi-adapter.ts",
     "eval:run:dev": "BRAINBENCH_N=1 bun eval/runner/multi-adapter.ts",
     "eval:world:view": "bun eval/cli/world-view.ts",
diff --git a/scripts/check-jsonb-pattern.sh b/scripts/check-jsonb-pattern.sh
new file mode 100755
index 000000000..16e211eb2
--- /dev/null
+++ b/scripts/check-jsonb-pattern.sh
@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+# CI guard: fail if any source file uses the buggy `${JSON.stringify(x)}::jsonb`
+# template-string pattern instead of postgres.js's `sql.json(x)`.
+#
+# This is best-effort static analysis. It catches the common copy-paste form
+# that caused the v0.12.0 silent-data-loss bug (JSONB columns stored as
+# string literals on Postgres while PGLite hid the bug). Multi-line and
+# helper-wrapped variants are NOT caught here — those are covered by
+# test/e2e/postgres-jsonb.test.ts which round-trips actual writes through
+# real Postgres and asserts `frontmatter->>'k'` returns objects, not strings.
+#
+# Usage: scripts/check-jsonb-pattern.sh
+# Exit:  0 when no matches, 1 when matches found.
+
+set -euo pipefail
+
+ROOT="$(git rev-parse --show-toplevel 2>/dev/null || pwd)"
+cd "$ROOT"
+
+# Match the interpolated form: ${JSON.stringify(...)}::jsonb
+# Using grep -P for Perl-compatible regex (lookahead-free pattern is enough here).
+PATTERN='\$\{JSON\.stringify\([^)]*\)\}::jsonb'
+
+if grep -rEn "$PATTERN" src/ 2>/dev/null; then
+  echo
+  echo "ERROR: Found JSON.stringify(...)::jsonb pattern in src/."
+  echo "       postgres.js v3 stringifies again, producing JSONB string literals."
+  echo "       Use sql.json(x) instead. See feedback_postgres_jsonb_double_encode.md."
+  exit 1
+fi
+
+echo "OK: no JSON.stringify(x)::jsonb interpolation pattern in src/"
diff --git a/skills/migrate/SKILL.md b/skills/migrate/SKILL.md
index 78ad36e4c..55c6f0e9f 100644
--- a/skills/migrate/SKILL.md
+++ b/skills/migrate/SKILL.md
@@ -50,10 +50,17 @@ Universal migration from any wiki, note tool, or brain system into GBrain.
 ## Obsidian Migration
 
 1. Import the vault directory into gbrain (Obsidian vaults are markdown directories)
-2. Convert `[[wikilinks]]` to gbrain links:
-   - Read each page from gbrain
-   - For each `[[Name]]` found, resolve to a slug and create a link in gbrain
-   - `[[Name|alias]]` uses the alias for context
+2. Wire the graph with native wikilink support (v0.12.1+):
+
+   ```bash
+   gbrain extract links --source db --dry-run | head -20    # preview
+   gbrain extract links --source db                         # commit
+   ```
+
+   `extract links` natively parses `[[relative/path]]` and `[[relative/path|Display Text]]`
+   alongside standard `[text](page.md)` markdown syntax. Ancestor-search resolution handles
+   wiki KBs where authors omit one or more leading `../` prefixes. The `.md` suffix is
+   inferred automatically for wikilinks.
 
 Obsidian-specific:
 - Tags (`#tag`) become gbrain tags
diff --git a/skills/migrations/v0.12.1.md b/skills/migrations/v0.12.1.md
new file mode 100644
index 000000000..f325ef61f
--- /dev/null
+++ b/skills/migrations/v0.12.1.md
@@ -0,0 +1,107 @@
+# v0.12.1 Migration: Extract Performance + Migration Timeout Fix
+
+This release is a pure performance bug fix. **No manual steps are needed for most
+users** — re-run `gbrain init --migrate-only` and re-run `gbrain extract all` if
+desired. Both should now complete successfully on any brain size.
+
+## What changed
+
+Two production-blocking bugs are fixed:
+
+1. **`gbrain extract` no longer hangs on large brains.** The N+1 dedup pre-load
+   that ran 47K serial `getLinks()` calls before any work started is gone. Both
+   engines already enforced uniqueness at the SQL layer; the in-memory dedup was
+   redundant. Combined with new batched 100-row INSERTs, a full re-extract on a
+   47K-page brain drops from "10+ min hang then ~minutes more" to "immediate
+   work, ~30-60s total."
+
+2. **v0.12.0 schema migration no longer times out on duplicate-heavy brains.**
+   Migration v9 (timeline_dedup_index) and v8 (links uniqueness) now pre-create
+   a btree helper index before the `DELETE ... USING` self-join, then drop it
+   after dedup. Turns O(n²) dedup into O(n log n). On 80K+ duplicate rows the
+   migration completes in under a second instead of timing out at 60 seconds.
+
+## What you need to do
+
+### If your v0.12.0 upgrade succeeded — you're already done
+
+The migration is idempotent. The fix only matters if your migration FAILED on
+the v0.12.0 upgrade attempt. Run `gbrain init --migrate-only` once to confirm
+your schema is at version 10, then run `gbrain extract all --dir <brain>` if
+you want to reuse it now that it's fast.
+
+### If your v0.12.0 upgrade FAILED on `idx_timeline_dedup` creation
+
+You may have the brain in a partial-migration state with duplicate rows in
+`timeline_entries` (or `links`). Run:
+
+```bash
+gbrain init --migrate-only
+```
+
+Migration v9 will pre-create the helper index, dedup any existing duplicates
+(now sub-second instead of timing out), drop the helper, and create the unique
+index. Idempotent — safe to re-run.
+
+If you previously ran the manual `CREATE TABLE _clean AS SELECT DISTINCT ON
+... + table swap` workaround Garry posted, your schema should already be at
+version 10. Confirm with:
+
+```bash
+gbrain config get version
+```
+
+If it shows `10`, you're done.
+
+### If you previously did manual SQL surgery on duplicate timeline rows
+
+The unique index `idx_timeline_dedup` should now be present after the workaround.
+Re-running `gbrain init --migrate-only` is a no-op for v9 (uses
+`CREATE UNIQUE INDEX IF NOT EXISTS`). The new migration code adds the helper
+btree on the dedup columns first — but the helper is dropped at the end of the
+migration, so even if v9 re-ran (it won't, version is already at 10), it would
+leave your schema unchanged.
+
+### Re-running `gbrain extract` on a previously-stuck brain
+
+This is the most common case. Run:
+
+```bash
+gbrain extract all --dir <brain-dir>
+# or for live brains with no local checkout:
+gbrain extract all --source db
+```
+
+Expect immediate output (`Links: created N from M pages` lines streaming as files
+process), not a 10-minute hang. On a re-run of a fully-extracted brain you should
+see `Done: 0 links, 0 timeline entries from N pages` — that's the truthful counter
+at work, confirming nothing changed.
+
+## New engine API (informational, optional)
+
+For plugin authors building integrations on the `BrainEngine` interface, two
+new methods are available:
+
+- `addLinksBatch(LinkBatchInput[]) → Promise<number>`
+- `addTimelineEntriesBatch(TimelineBatchInput[]) → Promise<number>`
+
+Both return the count of rows actually inserted (excluding ON CONFLICT no-ops
+and JOIN-dropped rows whose slugs don't exist). Existing per-row `addLink` /
+`addTimelineEntry` are unchanged — no migration required for plugin code.
+
+## Verification
+
+After the migration completes:
+
+```bash
+# Confirm schema version
+gbrain config get version
+# Expect: 10
+
+# Confirm the unique indexes exist (Postgres / Supabase only)
+gbrain stats
+# Expect: link_count and timeline_entry_count both populated, no duplicates
+```
+
+If you hit any issue, file at https://github.com/garrytan/gbrain/issues with the
+output of `gbrain init --migrate-only` and `gbrain config get version`.
diff --git a/src/cli.ts b/src/cli.ts
index bee3da91c..d31044cea 100644
--- a/src/cli.ts
+++ b/src/cli.ts
@@ -18,7 +18,7 @@ for (const op of operations) {
 }
 
 // CLI-only commands that bypass the operation layer
-const CLI_ONLY = new Set(['init', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'features', 'autopilot', 'graph-query', 'jobs', 'apply-migrations', 'skillpack-check']);
+const CLI_ONLY = new Set(['init', 'upgrade', 'post-upgrade', 'check-update', 'integrations', 'publish', 'check-backlinks', 'lint', 'report', 'import', 'export', 'files', 'embed', 'serve', 'call', 'config', 'doctor', 'migrate', 'eval', 'sync', 'extract', 'features', 'autopilot', 'graph-query', 'jobs', 'apply-migrations', 'skillpack-check', 'repair-jsonb']);
 
 async function main() {
   const args = process.argv.slice(2);
@@ -306,6 +306,11 @@ async function handleCliOnly(command: string, args: string[]) {
     await runApplyMigrations(args);
     return;
   }
+  if (command === 'repair-jsonb') {
+    const { runRepairJsonbCli } = await import('./commands/repair-jsonb.ts');
+    await runRepairJsonbCli(args);
+    return;
+  }
   if (command === 'skillpack-check') {
     // Agent-readable health report. Shells out to doctor + apply-migrations
     // internally; does not need its own DB connection.
diff --git a/src/commands/extract.ts b/src/commands/extract.ts
index 1b5abb7e6..b934ccff9 100644
--- a/src/commands/extract.ts
+++ b/src/commands/extract.ts
@@ -18,11 +18,18 @@
 
 import { readFileSync, readdirSync, lstatSync, existsSync } from 'fs';
 import { join, relative, dirname } from 'path';
-import type { BrainEngine } from '../core/engine.ts';
+import type { BrainEngine, LinkBatchInput, TimelineBatchInput } from '../core/engine.ts';
 import type { PageType } from '../core/types.ts';
 import { parseMarkdown } from '../core/markdown.ts';
 import { extractPageLinks, parseTimelineEntries, inferLinkType } from '../core/link-extraction.ts';
 
+// Batch size for addLinksBatch / addTimelineEntriesBatch.
+// Postgres bind-parameter limit is 65535. Links use 4 cols/row → 16K hard ceiling;
+// timeline uses 5 cols/row → 13K hard ceiling. 100 is conservative on round-trip
+// count but safe at any future schema width and keeps per-batch error blast radius
+// small (a malformed row aborts at most 100, not thousands).
+const BATCH_SIZE = 100;
+
 // --- Types ---
 
 export interface ExtractedLink {
@@ -69,19 +76,72 @@ export function walkMarkdownFiles(dir: string): { path: string; relPath: string
 
 // --- Link extraction ---
 
-/** Extract markdown links to .md files (relative paths only) */
+/**
+ * Extract markdown links to .md files (relative paths only).
+ *
+ * Handles two syntaxes:
+ *   1. Standard markdown:  [text](relative/path.md)
+ *   2. Wikilinks:          [[relative/path]] or [[relative/path|Display Text]]
+ *
+ * Both are resolved relative to the file that contains them. External URLs
+ * (containing ://) are always skipped. For wikilinks, the .md suffix is added
+ * if absent and section anchors (#heading) are stripped.
+ */
 export function extractMarkdownLinks(content: string): { name: string; relTarget: string }[] {
   const results: { name: string; relTarget: string }[] = [];
-  const pattern = /\[([^\]]+)\]\(([^)]+\.md)\)/g;
+
+  const mdPattern = /\[([^\]]+)\]\(([^)]+\.md)\)/g;
   let match;
-  while ((match = pattern.exec(content)) !== null) {
+  while ((match = mdPattern.exec(content)) !== null) {
     const target = match[2];
-    if (target.includes('://')) continue; // skip external URLs
+    if (target.includes('://')) continue;
     results.push({ name: match[1], relTarget: target });
   }
+
+  const wikiPattern = /\[\[([^|\]]+?)(?:\|[^\]]*?)?\]\]/g;
+  while ((match = wikiPattern.exec(content)) !== null) {
+    const rawPath = match[1].trim();
+    if (rawPath.includes('://')) continue;
+    const hashIdx = rawPath.indexOf('#');
+    const pagePath = hashIdx >= 0 ? rawPath.slice(0, hashIdx) : rawPath;
+    if (!pagePath) continue;
+    const relTarget = pagePath.endsWith('.md') ? pagePath : pagePath + '.md';
+    const pipeIdx = match[0].indexOf('|');
+    const displayName = pipeIdx >= 0 ? match[0].slice(pipeIdx + 1, -2).trim() : rawPath;
+    results.push({ name: displayName, relTarget });
+  }
+
   return results;
 }
 
+/**
+ * Resolve a wikilink target to a canonical slug, given the directory of the
+ * containing page and the set of all known slugs in the brain.
+ *
+ * Wiki KBs often use inconsistent relative depths. Authors omit one or more
+ * leading `../` because they think in "wiki-root-relative" terms. Resolution
+ * order (first match wins):
+ *   1. Standard `join(fileDir, relTarget)` — exact relative path as written
+ *   2. Ancestor search — strip leading path components from fileDir, retry
+ *
+ * Returns null when no matching slug is found (dangling link).
+ */
+export function resolveSlug(fileDir: string, relTarget: string, allSlugs: Set<string>): string | null {
+  const targetNoExt = relTarget.endsWith('.md') ? relTarget.slice(0, -3) : relTarget;
+
+  const s1 = join(fileDir, targetNoExt);
+  if (allSlugs.has(s1)) return s1;
+
+  const parts = fileDir.split('/').filter(Boolean);
+  for (let strip = 1; strip <= parts.length; strip++) {
+    const ancestor = parts.slice(0, parts.length - strip).join('/');
+    const candidate = ancestor ? join(ancestor, targetNoExt) : targetNoExt;
+    if (allSlugs.has(candidate)) return candidate;
+  }
+
+  return null;
+}
+
 /** Infer link type from directory structure */
 function inferLinkType(fromDir: string, toDir: string, frontmatter?: Record<string, unknown>): string {
   const from = fromDir.split('/')[0];
@@ -139,8 +199,8 @@ export function extractLinksFromFile(
   const fm = parseFrontmatterFromContent(content, relPath);
 
   for (const { name, relTarget } of extractMarkdownLinks(content)) {
-    const resolved = join(fileDir, relTarget).replace('.md', '');
-    if (allSlugs.has(resolved)) {
+    const resolved = resolveSlug(fileDir, relTarget, allSlugs);
+    if (resolved !== null) {
       links.push({
         from_slug: slug, to_slug: resolved,
         link_type: inferLinkType(fileDir, dirname(resolved), fm),
@@ -312,34 +372,42 @@ async function extractLinksFromDir(
   const files = walkMarkdownFiles(brainDir);
   const allSlugs = new Set(files.map(f => f.relPath.replace('.md', '')));
 
-  // Load existing links for O(1) dedup
-  const existing = new Set<string>();
-  try {
-    const pages = await engine.listPages({ limit: 100000 });
-    for (const page of pages) {
-      for (const link of await engine.getLinks(page.slug)) {
-        existing.add(`${link.from_slug}::${link.to_slug}`);
-      }
-    }
-  } catch { /* fresh brain */ }
+  // Dedup in dry-run only — DB enforces uniqueness via ON CONFLICT in batch writes.
+  // Without this, the same link extracted from N files would print N times in --dry-run.
+  const dryRunSeen = dryRun ? new Set<string>() : null;
 
   let created = 0;
+  const batch: LinkBatchInput[] = [];
+  async function flush() {
+    if (batch.length === 0) return;
+    try {
+      created += await engine.addLinksBatch(batch);
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      if (jsonMode) {
+        process.stderr.write(JSON.stringify({ event: 'batch_error', size: batch.length, error: msg }) + '\n');
+      } else {
+        console.error(`  batch error (${batch.length} link rows lost): ${msg}`);
+      }
+    } finally {
+      batch.length = 0;
+    }
+  }
+
   for (let i = 0; i < files.length; i++) {
     try {
       const content = readFileSync(files[i].path, 'utf-8');
       const links = extractLinksFromFile(content, files[i].relPath, allSlugs);
       for (const link of links) {
-        const key = `${link.from_slug}::${link.to_slug}`;
-        if (existing.has(key)) continue;
-        existing.add(key);
-        if (dryRun) {
+        if (dryRunSeen) {
+          const key = `${link.from_slug}::${link.to_slug}::${link.link_type}`;
+          if (dryRunSeen.has(key)) continue;
+          dryRunSeen.add(key);
           if (!jsonMode) console.log(`  ${link.from_slug} → ${link.to_slug} (${link.link_type})`);
           created++;
         } else {
-          try {
-            await engine.addLink(link.from_slug, link.to_slug, link.context, link.link_type);
-            created++;
-          } catch { /* UNIQUE or page not found */ }
+          batch.push(link);
+          if (batch.length >= BATCH_SIZE) await flush();
         }
       }
     } catch { /* skip unreadable */ }
@@ -347,6 +415,7 @@ async function extractLinksFromDir(
       process.stderr.write(JSON.stringify({ event: 'progress', phase: 'extracting_links', done: i + 1, total: files.length }) + '\n');
     }
   }
+  await flush();
 
   if (!jsonMode) {
     const label = dryRun ? '(dry run) would create' : 'created';
@@ -360,34 +429,41 @@ async function extractTimelineFromDir(
 ): Promise<{ created: number; pages: number }> {
   const files = walkMarkdownFiles(brainDir);
 
-  // Load existing timeline entries for O(1) dedup
-  const existing = new Set<string>();
-  try {
-    const pages = await engine.listPages({ limit: 100000 });
-    for (const page of pages) {
-      for (const entry of await engine.getTimeline(page.slug)) {
-        existing.add(`${page.slug}::${entry.date}::${entry.summary}`);
-      }
-    }
-  } catch { /* fresh brain */ }
+  // Dedup in dry-run only — DB enforces uniqueness via ON CONFLICT in batch writes.
+  const dryRunSeen = dryRun ? new Set<string>() : null;
 
   let created = 0;
+  const batch: TimelineBatchInput[] = [];
+  async function flush() {
+    if (batch.length === 0) return;
+    try {
+      created += await engine.addTimelineEntriesBatch(batch);
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      if (jsonMode) {
+        process.stderr.write(JSON.stringify({ event: 'batch_error', size: batch.length, error: msg }) + '\n');
+      } else {
+        console.error(`  batch error (${batch.length} timeline rows lost): ${msg}`);
+      }
+    } finally {
+      batch.length = 0;
+    }
+  }
+
   for (let i = 0; i < files.length; i++) {
     try {
       const content = readFileSync(files[i].path, 'utf-8');
       const slug = files[i].relPath.replace('.md', '');
       for (const entry of extractTimelineFromContent(content, slug)) {
-        const key = `${entry.slug}::${entry.date}::${entry.summary}`;
-        if (existing.has(key)) continue;
-        existing.add(key);
-        if (dryRun) {
+        if (dryRunSeen) {
+          const key = `${entry.slug}::${entry.date}::${entry.summary}`;
+          if (dryRunSeen.has(key)) continue;
+          dryRunSeen.add(key);
           if (!jsonMode) console.log(`  ${entry.slug}: ${entry.date} — ${entry.summary}`);
           created++;
         } else {
-          try {
-            await engine.addTimelineEntry(entry.slug, { date: entry.date, source: entry.source, summary: entry.summary, detail: entry.detail });
-            created++;
-          } catch { /* page not in DB or constraint */ }
+          batch.push({ slug: entry.slug, date: entry.date, source: entry.source, summary: entry.summary, detail: entry.detail });
+          if (batch.length >= BATCH_SIZE) await flush();
         }
       }
     } catch { /* skip unreadable */ }
@@ -395,6 +471,7 @@ async function extractTimelineFromDir(
       process.stderr.write(JSON.stringify({ event: 'progress', phase: 'extracting_timeline', done: i + 1, total: files.length }) + '\n');
     }
   }
+  await flush();
 
   if (!jsonMode) {
     const label = dryRun ? '(dry run) would create' : 'created';
@@ -455,6 +532,26 @@ async function extractLinksFromDB(
   const slugList = Array.from(allSlugs);
   let processed = 0, created = 0;
 
+  // Dedup in dry-run only — DB enforces uniqueness via ON CONFLICT in batch writes.
+  const dryRunSeen = dryRun ? new Set<string>() : null;
+
+  const batch: LinkBatchInput[] = [];
+  async function flush() {
+    if (batch.length === 0) return;
+    try {
+      created += await engine.addLinksBatch(batch);
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      if (jsonMode) {
+        process.stderr.write(JSON.stringify({ event: 'batch_error', size: batch.length, error: msg }) + '\n');
+      } else {
+        console.error(`  batch error (${batch.length} link rows lost): ${msg}`);
+      }
+    } finally {
+      batch.length = 0;
+    }
+  }
+
   for (let i = 0; i < slugList.length; i++) {
     const slug = slugList[i];
     const page = await engine.getPage(slug);
@@ -471,7 +568,10 @@ async function extractLinksFromDB(
 
     for (const c of candidates) {
       if (!allSlugs.has(c.targetSlug)) continue;
-      if (dryRun) {
+      if (dryRunSeen) {
+        const key = `${slug}::${c.targetSlug}::${c.linkType}`;
+        if (dryRunSeen.has(key)) continue;
+        dryRunSeen.add(key);
         if (jsonMode) {
           process.stdout.write(JSON.stringify({
             action: 'add_link', from: slug, to: c.targetSlug,
@@ -482,10 +582,8 @@ async function extractLinksFromDB(
         }
         created++;
       } else {
-        try {
-          await engine.addLink(slug, c.targetSlug, c.context, c.linkType);
-          created++;
-        } catch { /* FK violation or other */ }
+        batch.push({ from_slug: slug, to_slug: c.targetSlug, link_type: c.linkType, context: c.context });
+        if (batch.length >= BATCH_SIZE) await flush();
       }
     }
     processed++;
@@ -493,6 +591,7 @@ async function extractLinksFromDB(
       process.stderr.write(JSON.stringify({ event: 'progress', phase: 'extracting_links_db', done: processed, total: slugList.length }) + '\n');
     }
   }
+  await flush();
 
   if (!jsonMode) {
     const label = dryRun ? '(dry run) would create' : 'created';
@@ -512,6 +611,26 @@ async function extractTimelineFromDB(
   const slugList = Array.from(allSlugs);
   let processed = 0, created = 0;
 
+  // Dedup in dry-run only — DB enforces uniqueness via ON CONFLICT in batch writes.
+  const dryRunSeen = dryRun ? new Set<string>() : null;
+
+  const batch: TimelineBatchInput[] = [];
+  async function flush() {
+    if (batch.length === 0) return;
+    try {
+      created += await engine.addTimelineEntriesBatch(batch);
+    } catch (e) {
+      const msg = e instanceof Error ? e.message : String(e);
+      if (jsonMode) {
+        process.stderr.write(JSON.stringify({ event: 'batch_error', size: batch.length, error: msg }) + '\n');
+      } else {
+        console.error(`  batch error (${batch.length} timeline rows lost): ${msg}`);
+      }
+    } finally {
+      batch.length = 0;
+    }
+  }
+
   for (let i = 0; i < slugList.length; i++) {
     const slug = slugList[i];
     const page = await engine.getPage(slug);
@@ -527,7 +646,10 @@ async function extractTimelineFromDB(
     const entries = parseTimelineEntries(fullContent);
 
     for (const entry of entries) {
-      if (dryRun) {
+      if (dryRunSeen) {
+        const key = `${slug}::${entry.date}::${entry.summary}`;
+        if (dryRunSeen.has(key)) continue;
+        dryRunSeen.add(key);
         if (jsonMode) {
           process.stdout.write(JSON.stringify({
             action: 'add_timeline', slug, date: entry.date,
@@ -538,14 +660,8 @@ async function extractTimelineFromDB(
         }
         created++;
       } else {
-        try {
-          await engine.addTimelineEntry(
-            slug,
-            { date: entry.date, summary: entry.summary, detail: entry.detail || '' },
-            { skipExistenceCheck: true },
-          );
-          created++;
-        } catch { /* dedup constraint or other */ }
+        batch.push({ slug, date: entry.date, summary: entry.summary, detail: entry.detail || '' });
+        if (batch.length >= BATCH_SIZE) await flush();
       }
     }
     processed++;
@@ -553,6 +669,7 @@ async function extractTimelineFromDB(
       process.stderr.write(JSON.stringify({ event: 'progress', phase: 'extracting_timeline_db', done: processed, total: slugList.length }) + '\n');
     }
   }
+  await flush();
 
   if (!jsonMode) {
     const label = dryRun ? '(dry run) would create' : 'created';
diff --git a/src/commands/files.ts b/src/commands/files.ts
index 592728049..e6c5b3842 100644
--- a/src/commands/files.ts
+++ b/src/commands/files.ts
@@ -251,7 +251,7 @@ async function uploadRaw(args: string[]) {
   await sql`
     INSERT INTO files (page_slug, filename, storage_path, mime_type, size_bytes, content_hash, metadata)
     VALUES (${pageSlug}, ${filename}, ${storagePath}, ${mimeType}, ${stat.size}, ${'sha256:' + hash},
-            ${JSON.stringify({ type: fileType, upload_method: method })}::jsonb)
+            ${sql.json({ type: fileType, upload_method: method })})
     ON CONFLICT (storage_path) DO UPDATE SET
       content_hash = EXCLUDED.content_hash,
       size_bytes = EXCLUDED.size_bytes,
diff --git a/src/commands/migrations/index.ts b/src/commands/migrations/index.ts
index c84ca9aaa..a9f9e8e39 100644
--- a/src/commands/migrations/index.ts
+++ b/src/commands/migrations/index.ts
@@ -13,10 +13,12 @@
 import type { Migration } from './types.ts';
 import { v0_11_0 } from './v0_11_0.ts';
 import { v0_12_0 } from './v0_12_0.ts';
+import { v0_12_2 } from './v0_12_2.ts';
 
 export const migrations: Migration[] = [
   v0_11_0,
   v0_12_0,
+  v0_12_2,
 ];
 
 /** Look up a migration by exact version string. */
diff --git a/src/commands/migrations/v0_12_0.ts b/src/commands/migrations/v0_12_0.ts
index 363ba7e76..e396afa22 100644
--- a/src/commands/migrations/v0_12_0.ts
+++ b/src/commands/migrations/v0_12_0.ts
@@ -39,7 +39,10 @@ import { appendCompletedMigration } from '../../core/preferences.ts';
 function phaseASchema(opts: OrchestratorOpts): OrchestratorPhaseResult {
   if (opts.dryRun) return { name: 'schema', status: 'skipped', detail: 'dry-run' };
   try {
-    execSync('gbrain init --migrate-only', { stdio: 'inherit', timeout: 60_000, env: process.env });
+    // 10-minute budget. Migrations v8/v9 dedup with helper-index should be sub-second
+    // even on 80K-duplicate brains, but the outer wall-clock cap shouldn't be the
+    // failure mode (the prior 60s ceiling tripped Garry's production upgrade).
+    execSync('gbrain init --migrate-only', { stdio: 'inherit', timeout: 600_000, env: process.env });
     return { name: 'schema', status: 'complete' };
   } catch (e) {
     const msg = e instanceof Error ? e.message : String(e);
diff --git a/src/commands/migrations/v0_12_2.ts b/src/commands/migrations/v0_12_2.ts
new file mode 100644
index 000000000..bdb420622
--- /dev/null
+++ b/src/commands/migrations/v0_12_2.ts
@@ -0,0 +1,141 @@
+/**
+ * v0.12.2 migration orchestrator — JSONB double-encode repair.
+ *
+ * v0.12.0-and-earlier wrote JSONB columns via the buggy
+ * `JSON.stringify(value)`-then-cast-to-jsonb interpolation pattern, which
+ * postgres.js v3 stringified again on the wire. Result: every
+ * `frontmatter->>'key'` query returned NULL on Postgres-backed brains and
+ * GIN indexes on JSONB columns were inert. PGLite was unaffected (its
+ * driver path uses parameterized binding, never interpolation).
+ *
+ * v0.12.2 fixes the writes (sql.json) AND repairs existing rows in place.
+ * This is the migration. It's idempotent (only touches `jsonb_typeof = 'string'`
+ * rows) and safe to re-run. PGLite engines no-op cleanly.
+ *
+ * Phases (all idempotent):
+ *   A. Schema   — gbrain init --migrate-only (no schema changes in v0.12.2
+ *                 but we still apply for consistency with v0.12.0).
+ *   B. Repair   — gbrain repair-jsonb (the actual JSONB fix).
+ *   C. Verify   — gbrain repair-jsonb --dry-run --json; assert 0 remaining.
+ *   D. Record   — append completed.jsonl.
+ */
+
+import { execSync } from 'child_process';
+import type { Migration, OrchestratorOpts, OrchestratorResult, OrchestratorPhaseResult } from './types.ts';
+import { appendCompletedMigration } from '../../core/preferences.ts';
+
+// ── Phase A — Schema ────────────────────────────────────────
+
+function phaseASchema(opts: OrchestratorOpts): OrchestratorPhaseResult {
+  if (opts.dryRun) return { name: 'schema', status: 'skipped', detail: 'dry-run' };
+  try {
+    execSync('gbrain init --migrate-only', { stdio: 'inherit', timeout: 60_000, env: process.env });
+    return { name: 'schema', status: 'complete' };
+  } catch (e) {
+    const msg = e instanceof Error ? e.message : String(e);
+    return { name: 'schema', status: 'failed', detail: msg };
+  }
+}
+
+// ── Phase B — JSONB repair ──────────────────────────────────
+
+function phaseBRepair(opts: OrchestratorOpts): OrchestratorPhaseResult {
+  if (opts.dryRun) return { name: 'jsonb_repair', status: 'skipped', detail: 'dry-run' };
+  try {
+    execSync('gbrain repair-jsonb', { stdio: 'inherit', timeout: 600_000, env: process.env });
+    return { name: 'jsonb_repair', status: 'complete' };
+  } catch (e) {
+    const msg = e instanceof Error ? e.message : String(e);
+    return { name: 'jsonb_repair', status: 'failed', detail: msg };
+  }
+}
+
+// ── Phase C — Verify ────────────────────────────────────────
+
+function phaseCVerify(opts: OrchestratorOpts): OrchestratorPhaseResult {
+  if (opts.dryRun) return { name: 'verify', status: 'skipped', detail: 'dry-run' };
+  try {
+    const out = execSync('gbrain repair-jsonb --dry-run --json', {
+      encoding: 'utf-8', timeout: 60_000, env: process.env,
+    });
+    const parsed = JSON.parse(out) as { total_repaired?: number; engine?: string };
+    const remaining = parsed.total_repaired ?? 0;
+    if (remaining > 0) {
+      return {
+        name: 'verify',
+        status: 'failed',
+        detail: `${remaining} string-typed JSONB rows remain after repair`,
+      };
+    }
+    return { name: 'verify', status: 'complete', detail: parsed.engine ? `engine=${parsed.engine}` : undefined };
+  } catch (e) {
+    const msg = e instanceof Error ? e.message : String(e);
+    return { name: 'verify', status: 'failed', detail: msg };
+  }
+}
+
+// ── Orchestrator ────────────────────────────────────────────
+
+async function orchestrator(opts: OrchestratorOpts): Promise<OrchestratorResult> {
+  console.log('');
+  console.log('=== v0.12.2 — JSONB double-encode repair ===');
+  if (opts.dryRun) console.log('  (dry-run; no side effects)');
+  console.log('');
+
+  const phases: OrchestratorPhaseResult[] = [];
+
+  const a = phaseASchema(opts);
+  phases.push(a);
+  if (a.status === 'failed') return finalizeResult(phases, 'failed');
+
+  const b = phaseBRepair(opts);
+  phases.push(b);
+  if (b.status === 'failed') return finalizeResult(phases, 'failed');
+
+  const c = phaseCVerify(opts);
+  phases.push(c);
+
+  const overallStatus: 'complete' | 'partial' | 'failed' =
+    a.status === 'failed' || b.status === 'failed' ? 'failed' :
+    c.status === 'failed' ? 'partial' :
+    'complete';
+
+  return finalizeResult(phases, overallStatus);
+}
+
+function finalizeResult(phases: OrchestratorPhaseResult[], status: 'complete' | 'partial' | 'failed'): OrchestratorResult {
+  if (status !== 'failed') {
+    try {
+      appendCompletedMigration({ version: '0.12.2', status: status as 'complete' | 'partial' });
+    } catch {
+      // Recording is best-effort.
+    }
+  }
+  return {
+    version: '0.12.2',
+    status,
+    phases,
+  };
+}
+
+export const v0_12_2: Migration = {
+  version: '0.12.2',
+  featurePitch: {
+    headline: 'Postgres frontmatter queries now work — JSONB double-encode bug fixed and existing rows auto-repaired',
+    description:
+      'gbrain v0.12.0-and-earlier silently stored JSONB columns as quoted string literals on ' +
+      'Postgres/Supabase (PGLite was unaffected). Every `frontmatter->>\'key\'` returned NULL ' +
+      'and GIN indexes were inert. v0.12.2 fixes the writes AND auto-repairs every existing ' +
+      'string-typed row in pages.frontmatter, raw_data.data, ingest_log.pages_updated, ' +
+      'files.metadata, and page_versions.frontmatter. The migration is idempotent. Pages ' +
+      'truncated by the splitBody horizontal-rule bug can be recovered with `gbrain sync --full`.',
+  },
+  orchestrator,
+};
+
+/** Exported for unit tests. */
+export const __testing = {
+  phaseASchema,
+  phaseBRepair,
+  phaseCVerify,
+};
diff --git a/src/commands/repair-jsonb.ts b/src/commands/repair-jsonb.ts
new file mode 100644
index 000000000..a028f43c5
--- /dev/null
+++ b/src/commands/repair-jsonb.ts
@@ -0,0 +1,151 @@
+/**
+ * `gbrain repair-jsonb` — repair JSONB columns that were stored as string
+ * literals due to the v0.12.0-and-earlier double-encode bug.
+ *
+ * Background: postgres-engine.ts wrote frontmatter and other JSONB columns
+ * via the buggy `JSON.stringify(value)`-then-cast-to-jsonb interpolation
+ * pattern, which postgres.js v3 stringified AGAIN on the wire. Result: every `frontmatter->>'key'` query returned NULL
+ * on Postgres-backed brains; GIN indexes were inert. PGLite was unaffected
+ * (different driver path). v0.12.1 fixes the writes (sql.json) but existing
+ * rows stay broken until they're rewritten — that's what this command does.
+ *
+ * Strategy: for each affected JSONB column, detect rows where
+ * `jsonb_typeof(col) = 'string'` and rewrite them via `(col #>> '{}')::jsonb`,
+ * which extracts the string payload and re-parses it as JSONB. Idempotent:
+ * re-running is a no-op (no rows match the guard). PGLite is a no-op too
+ * (it never wrote string-typed JSONB).
+ *
+ * Affected columns (audit of src/schema.sql):
+ *   - pages.frontmatter           (postgres-engine.ts:107 putPage)
+ *   - raw_data.data               (postgres-engine.ts:668 putRawData)
+ *   - ingest_log.pages_updated    (postgres-engine.ts:846 logIngest)
+ *   - files.metadata              (commands/files.ts:254 file upload)
+ *   - page_versions.frontmatter   (downstream of pages.frontmatter via
+ *                                  INSERT...SELECT FROM pages)
+ *
+ * Other JSONB columns (minion_jobs.{data,result,progress,stacktrace},
+ * minion_inbox.payload) were always written via parameterized form ($N::jsonb
+ * with a string parameter, not interpolation) so they were never affected.
+ */
+
+import { loadConfig, toEngineConfig } from '../core/config.ts';
+import type { EngineConfig } from '../core/types.ts';
+import * as db from '../core/db.ts';
+
+interface RepairTarget {
+  table: string;
+  column: string;
+  /** Optional secondary key column for logging. */
+  keyCol?: string;
+}
+
+const TARGETS: RepairTarget[] = [
+  { table: 'pages',          column: 'frontmatter',    keyCol: 'slug' },
+  { table: 'raw_data',       column: 'data',           keyCol: 'source' },
+  { table: 'ingest_log',     column: 'pages_updated',  keyCol: 'source_ref' },
+  { table: 'files',          column: 'metadata',       keyCol: 'storage_path' },
+  { table: 'page_versions',  column: 'frontmatter',    keyCol: 'snapshot_at' },
+];
+
+export interface RepairResult {
+  engine: string;
+  per_target: Array<{
+    table: string;
+    column: string;
+    rows_repaired: number;
+  }>;
+  total_repaired: number;
+}
+
+export interface RepairOpts {
+  dryRun: boolean;
+  /** Engine config override (for tests). Defaults to loadConfig() result. */
+  engineConfig?: EngineConfig;
+}
+
+/**
+ * Run the repair against the currently-configured engine.
+ *
+ * On PGLite this finds 0 rows (the bug never affected the parameterized
+ * encode path PGLite uses) and exits cleanly. On Postgres it issues one
+ * idempotent UPDATE per target column.
+ */
+export async function repairJsonb(opts: RepairOpts = { dryRun: false }): Promise<RepairResult> {
+  let engineCfg = opts.engineConfig;
+  if (!engineCfg) {
+    const config = loadConfig();
+    if (!config) {
+      throw new Error('No brain configured. Run: gbrain init');
+    }
+    engineCfg = toEngineConfig(config);
+  }
+  const engineKind = engineCfg.engine || 'postgres';
+
+  const result: RepairResult = {
+    engine: engineKind,
+    per_target: [],
+    total_repaired: 0,
+  };
+
+  if (engineKind === 'pglite') {
+    for (const t of TARGETS) {
+      result.per_target.push({ table: t.table, column: t.column, rows_repaired: 0 });
+    }
+    return result;
+  }
+
+  await db.connect(engineCfg);
+  const sql = db.getConnection();
+
+  for (const t of TARGETS) {
+    let repaired = 0;
+
+    if (opts.dryRun) {
+      const rows = await sql.unsafe(
+        `SELECT count(*)::int AS n FROM ${t.table} WHERE jsonb_typeof(${t.column}) = 'string'`,
+      );
+      repaired = (rows[0] as { n: number }).n;
+    } else {
+      const rows = await sql.unsafe(
+        `UPDATE ${t.table}
+         SET ${t.column} = (${t.column} #>> '{}')::jsonb
+         WHERE jsonb_typeof(${t.column}) = 'string'
+         RETURNING 1`,
+      );
+      repaired = rows.length;
+    }
+
+    result.per_target.push({ table: t.table, column: t.column, rows_repaired: repaired });
+    result.total_repaired += repaired;
+  }
+
+  return result;
+}
+
+export async function runRepairJsonbCli(args: string[]): Promise<void> {
+  const dryRun = args.includes('--dry-run');
+  const jsonMode = args.includes('--json');
+
+  const result = await repairJsonb({ dryRun });
+
+  if (jsonMode) {
+    console.log(JSON.stringify({ status: 'ok', dry_run: dryRun, ...result }));
+    return;
+  }
+
+  if (result.engine === 'pglite') {
+    console.log('Engine: pglite — JSONB double-encode bug never affected this path. No-op.');
+    return;
+  }
+
+  console.log(`${dryRun ? '[dry-run] ' : ''}Engine: postgres`);
+  console.log(`${dryRun ? '[dry-run] ' : ''}JSONB repair across ${TARGETS.length} columns:`);
+  for (const t of result.per_target) {
+    const verb = dryRun ? 'would repair' : 'repaired';
+    console.log(`  ${t.table}.${t.column}: ${verb} ${t.rows_repaired} rows`);
+  }
+  console.log(`${dryRun ? '[dry-run] ' : ''}Total ${dryRun ? 'to repair' : 'repaired'}: ${result.total_repaired} rows`);
+  if (!dryRun && result.total_repaired === 0) {
+    console.log('Nothing to repair (already-valid JSONB or fresh install).');
+  }
+}
diff --git a/src/core/engine.ts b/src/core/engine.ts
index ec3ceb6a7..b2a4ee7cc 100644
--- a/src/core/engine.ts
+++ b/src/core/engine.ts
@@ -11,6 +11,23 @@ import type {
   EngineConfig,
 } from './types.ts';
 
+/** Input row for addLinksBatch. Optional fields default to '' (matches NOT NULL DDL). */
+export interface LinkBatchInput {
+  from_slug: string;
+  to_slug: string;
+  link_type?: string;
+  context?: string;
+}
+
+/** Input row for addTimelineEntriesBatch. Optional fields default to '' (matches NOT NULL DDL). */
+export interface TimelineBatchInput {
+  slug: string;
+  date: string;
+  source?: string;
+  summary: string;
+  detail?: string;
+}
+
 /** Maximum results returned by search operations. Internal bulk operations (listPages) are not clamped. */
 export const MAX_SEARCH_LIMIT = 100;
 
@@ -53,6 +70,13 @@ export interface BrainEngine {
 
   // Links
   addLink(from: string, to: string, context?: string, linkType?: string): Promise<void>;
+  /**
+   * Bulk insert links via a single multi-row INSERT...SELECT FROM (VALUES) JOIN pages
+   * statement with ON CONFLICT DO NOTHING. Returns the count of rows actually inserted
+   * (RETURNING clause excludes conflicts and JOIN-dropped rows whose slugs don't exist).
+   * Used by extract.ts to avoid 47K sequential round-trips on large brains.
+   */
+  addLinksBatch(links: LinkBatchInput[]): Promise<number>;
   /**
    * Remove links from `from` to `to`. If linkType is provided, only that specific
    * (from, to, type) row is removed. If omitted, ALL link types between the pair
@@ -98,6 +122,13 @@ export interface BrainEngine {
     entry: TimelineInput,
     opts?: { skipExistenceCheck?: boolean },
   ): Promise<void>;
+  /**
+   * Bulk insert timeline entries via a single multi-row INSERT...SELECT FROM (VALUES)
+   * JOIN pages statement with ON CONFLICT DO NOTHING. Returns the count of rows
+   * actually inserted (RETURNING excludes conflicts and JOIN-dropped rows whose
+   * slugs don't exist). Used by extract.ts to avoid sequential round-trips.
+   */
+  addTimelineEntriesBatch(entries: TimelineBatchInput[]): Promise<number>;
   getTimeline(slug: string, opts?: TimelineOpts): Promise<TimelineEntry[]>;
 
   // Raw data
diff --git a/src/core/markdown.ts b/src/core/markdown.ts
index 239fe054c..0b7f13b68 100644
--- a/src/core/markdown.ts
+++ b/src/core/markdown.ts
@@ -22,14 +22,16 @@ export interface ParsedMarkdown {
  *   tags: [startups, growth]
  *   ---
  *   Compiled truth content here...
- *   ---
+ *
+ *   <!-- timeline -->
  *   Timeline content here...
  *
  * The first --- pair is YAML frontmatter (handled by gray-matter).
- * After frontmatter, the body is split at the first standalone ---
- * (a line containing only --- with optional whitespace).
- * Everything before is compiled_truth, everything after is timeline.
- * If no body --- exists, all content is compiled_truth.
+ * After frontmatter, the body is split at the first recognized timeline
+ * sentinel: `<!-- timeline -->` (preferred), `--- timeline ---` (decorated),
+ * or a plain `---` immediately preceding a `## Timeline` / `## History`
+ * heading (backward-compat for existing files). A bare `---` in body text
+ * is treated as a markdown horizontal rule, not a timeline separator.
  */
 export function parseMarkdown(content: string, filePath?: string): ParsedMarkdown {
   const { data: frontmatter, content: body } = matter(content);
@@ -62,26 +64,21 @@ export function parseMarkdown(content: string, filePath?: string): ParsedMarkdow
 }
 
 /**
- * Split body content at first standalone --- separator.
+ * Split body content at the first recognized timeline sentinel.
  * Returns compiled_truth (before) and timeline (after).
+ *
+ * Recognized sentinels (in order of precedence):
+ *   1. `<!-- timeline -->` — preferred, unambiguous, what serializeMarkdown emits
+ *   2. `--- timeline ---` — decorated separator
+ *   3. `---` ONLY when the next non-empty line is `## Timeline` or `## History`
+ *      (backward-compat fallback for older gbrain-written files)
+ *
+ * A plain `---` line is a markdown horizontal rule, NOT a timeline separator.
+ * Treating bare `---` as a separator caused 83% content truncation on wiki corpora.
  */
 export function splitBody(body: string): { compiled_truth: string; timeline: string } {
-  // Match a line that is only --- (with optional whitespace)
-  // Must not be at the very start (that would be frontmatter)
   const lines = body.split('\n');
-  let splitIndex = -1;
-
-  for (let i = 0; i < lines.length; i++) {
-    const trimmed = lines[i].trim();
-    if (trimmed === '---') {
-      // Skip if this is the very first non-empty line (leftover from frontmatter parsing)
-      const beforeContent = lines.slice(0, i).join('\n').trim();
-      if (beforeContent.length > 0) {
-        splitIndex = i;
-        break;
-      }
-    }
-  }
+  const splitIndex = findTimelineSplitIndex(lines);
 
   if (splitIndex === -1) {
     return { compiled_truth: body, timeline: '' };
@@ -92,6 +89,33 @@ export function splitBody(body: string): { compiled_truth: string; timeline: str
   return { compiled_truth, timeline };
 }
 
+function findTimelineSplitIndex(lines: string[]): number {
+  for (let i = 0; i < lines.length; i++) {
+    const trimmed = lines[i].trim();
+
+    if (trimmed === '<!-- timeline -->' || trimmed === '<!--timeline-->') {
+      return i;
+    }
+
+    if (trimmed === '--- timeline ---' || /^---\s+timeline\s+---$/i.test(trimmed)) {
+      return i;
+    }
+
+    if (trimmed === '---') {
+      const beforeContent = lines.slice(0, i).join('\n').trim();
+      if (beforeContent.length === 0) continue;
+
+      for (let j = i + 1; j < lines.length; j++) {
+        const next = lines[j].trim();
+        if (next.length === 0) continue;
+        if (/^##\s+(timeline|history)\b/i.test(next)) return i;
+        break;
+      }
+    }
+  }
+  return -1;
+}
+
 /**
  * Serialize a page back to markdown format.
  * Produces: frontmatter + compiled_truth + --- + timeline
@@ -116,7 +140,7 @@ export function serializeMarkdown(
 
   let body = compiled_truth;
   if (timeline) {
-    body += '\n\n---\n\n' + timeline;
+    body += '\n\n<!-- timeline -->\n\n' + timeline;
   }
 
   return yamlContent + '\n\n' + body + '\n';
@@ -125,8 +149,18 @@ export function serializeMarkdown(
 function inferType(filePath?: string): PageType {
   if (!filePath) return 'concept';
 
-  // Normalize: add leading / for consistent matching
+  // Normalize: add leading / for consistent matching.
+  // Wiki subtypes and /writing/ check FIRST — they're stronger signals than
+  // ancestor directories. e.g. `projects/blog/writing/essay.md` is a piece of
+  // writing, not a project page; `tech/wiki/analysis/foo.md` is analysis,
+  // not a hit on the broader `tech/` ancestor.
   const lower = ('/' + filePath).toLowerCase();
+  if (lower.includes('/writing/')) return 'writing';
+  if (lower.includes('/wiki/analysis/')) return 'analysis';
+  if (lower.includes('/wiki/guides/') || lower.includes('/wiki/guide/')) return 'guide';
+  if (lower.includes('/wiki/hardware/')) return 'hardware';
+  if (lower.includes('/wiki/architecture/')) return 'architecture';
+  if (lower.includes('/wiki/concepts/') || lower.includes('/wiki/concept/')) return 'concept';
   if (lower.includes('/people/') || lower.includes('/person/')) return 'person';
   if (lower.includes('/companies/') || lower.includes('/company/')) return 'company';
   if (lower.includes('/deals/') || lower.includes('/deal/')) return 'deal';
diff --git a/src/core/migrate.ts b/src/core/migrate.ts
index bfc5f047d..71f77d8a7 100644
--- a/src/core/migrate.ts
+++ b/src/core/migrate.ts
@@ -23,7 +23,9 @@ interface Migration {
 
 // Migrations are embedded here, not loaded from files.
 // Add new migrations at the end. Never modify existing ones.
-const MIGRATIONS: Migration[] = [
+// Exported for tests that structurally assert migration contents (e.g., "v9 must
+// pre-create idx_timeline_dedup_helper before the DELETE..."). Read-only contract.
+export const MIGRATIONS: Migration[] = [
   // Version 1 is the baseline (schema.sql creates everything with IF NOT EXISTS).
   {
     version: 2,
@@ -230,14 +232,20 @@ const MIGRATIONS: Migration[] = [
     // Idempotent for both upgrade and fresh-install paths.
     // Fresh installs already have links_from_to_type_unique from schema.sql; we drop it
     // (along with the legacy from-to-only constraint) before re-adding it cleanly.
+    // Helper btree on the dedup columns turns the DELETE...USING self-join from O(n²)
+    // into O(n log n). Without it, a brain with 80K+ duplicate link rows hits
+    // Supabase Management API's 60s ceiling during upgrade.
     sql: `
       ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_page_id_to_page_id_key;
       ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_unique;
+      CREATE INDEX IF NOT EXISTS idx_links_dedup_helper
+        ON links(from_page_id, to_page_id, link_type);
       DELETE FROM links a USING links b
         WHERE a.from_page_id = b.from_page_id
           AND a.to_page_id = b.to_page_id
           AND a.link_type = b.link_type
           AND a.id > b.id;
+      DROP INDEX IF EXISTS idx_links_dedup_helper;
       ALTER TABLE links ADD CONSTRAINT links_from_to_type_unique
         UNIQUE(from_page_id, to_page_id, link_type);
     `,
@@ -247,12 +255,18 @@ const MIGRATIONS: Migration[] = [
     name: 'timeline_dedup_index',
     // Idempotent: CREATE UNIQUE INDEX IF NOT EXISTS handles fresh + upgrade.
     // Dedup any existing duplicates first so the index can be created.
+    // Helper btree turns the DELETE...USING self-join from O(n²) into O(n log n).
+    // Without it, a brain with 80K+ duplicate timeline rows hits Supabase
+    // Management API's 60s ceiling. See migration v8 for the same pattern.
     sql: `
+      CREATE INDEX IF NOT EXISTS idx_timeline_dedup_helper
+        ON timeline_entries(page_id, date, summary);
       DELETE FROM timeline_entries a USING timeline_entries b
         WHERE a.page_id = b.page_id
           AND a.date = b.date
           AND a.summary = b.summary
           AND a.id > b.id;
+      DROP INDEX IF EXISTS idx_timeline_dedup_helper;
       CREATE UNIQUE INDEX IF NOT EXISTS idx_timeline_dedup
         ON timeline_entries(page_id, date, summary);
     `,
diff --git a/src/core/pglite-engine.ts b/src/core/pglite-engine.ts
index b2de9b52f..cceb6bf65 100644
--- a/src/core/pglite-engine.ts
+++ b/src/core/pglite-engine.ts
@@ -2,7 +2,7 @@ import { PGlite } from '@electric-sql/pglite';
 import { vector } from '@electric-sql/pglite/vector';
 import { pg_trgm } from '@electric-sql/pglite/contrib/pg_trgm';
 import type { Transaction } from '@electric-sql/pglite';
-import type { BrainEngine } from './engine.ts';
+import type { BrainEngine, LinkBatchInput, TimelineBatchInput } from './engine.ts';
 import { MAX_SEARCH_LIMIT, clampSearchLimit } from './engine.ts';
 import { runMigrations } from './migrate.ts';
 import { PGLITE_SCHEMA_SQL } from './pglite-schema.ts';
@@ -333,6 +333,29 @@ export class PGLiteEngine implements BrainEngine {
     );
   }
 
+  async addLinksBatch(links: LinkBatchInput[]): Promise<number> {
+    if (links.length === 0) return 0;
+    // unnest() pattern: 4 array-typed bound parameters regardless of batch size.
+    // Same shape as PostgresEngine. Avoids the 65535-parameter cap entirely.
+    const fromSlugs = links.map(l => l.from_slug);
+    const toSlugs = links.map(l => l.to_slug);
+    // Normalize optional fields to '' to match per-row addLink + NOT NULL DDL.
+    const linkTypes = links.map(l => l.link_type || '');
+    const contexts = links.map(l => l.context || '');
+    const result = await this.db.query(
+      `INSERT INTO links (from_page_id, to_page_id, link_type, context)
+       SELECT f.id, t.id, v.link_type, v.context
+       FROM unnest($1::text[], $2::text[], $3::text[], $4::text[])
+         AS v(from_slug, to_slug, link_type, context)
+       JOIN pages f ON f.slug = v.from_slug
+       JOIN pages t ON t.slug = v.to_slug
+       ON CONFLICT (from_page_id, to_page_id, link_type) DO NOTHING
+       RETURNING 1`,
+      [fromSlugs, toSlugs, linkTypes, contexts]
+    );
+    return result.rows.length;
+  }
+
   async removeLink(from: string, to: string, linkType?: string): Promise<void> {
     if (linkType !== undefined) {
       await this.db.query(
@@ -593,6 +616,28 @@ export class PGLiteEngine implements BrainEngine {
     );
   }
 
+  async addTimelineEntriesBatch(entries: TimelineBatchInput[]): Promise<number> {
+    if (entries.length === 0) return 0;
+    // unnest() pattern: 5 array-typed bound parameters regardless of batch size.
+    const slugs = entries.map(e => e.slug);
+    const dates = entries.map(e => e.date);
+    // Normalize optional fields to '' to match per-row addTimelineEntry + NOT NULL DDL.
+    const sources = entries.map(e => e.source || '');
+    const summaries = entries.map(e => e.summary);
+    const details = entries.map(e => e.detail || '');
+    const result = await this.db.query(
+      `INSERT INTO timeline_entries (page_id, date, source, summary, detail)
+       SELECT p.id, v.date::date, v.source, v.summary, v.detail
+       FROM unnest($1::text[], $2::text[], $3::text[], $4::text[], $5::text[])
+         AS v(slug, date, source, summary, detail)
+       JOIN pages p ON p.slug = v.slug
+       ON CONFLICT (page_id, date, summary) DO NOTHING
+       RETURNING 1`,
+      [slugs, dates, sources, summaries, details]
+    );
+    return result.rows.length;
+  }
+
   async getTimeline(slug: string, opts?: TimelineOpts): Promise<TimelineEntry[]> {
     const limit = opts?.limit || 100;
 
diff --git a/src/core/postgres-engine.ts b/src/core/postgres-engine.ts
index a22aa5871..04ef3803b 100644
--- a/src/core/postgres-engine.ts
+++ b/src/core/postgres-engine.ts
@@ -1,5 +1,5 @@
 import postgres from 'postgres';
-import type { BrainEngine } from './engine.ts';
+import type { BrainEngine, LinkBatchInput, TimelineBatchInput } from './engine.ts';
 import { MAX_SEARCH_LIMIT, clampSearchLimit } from './engine.ts';
 import { runMigrations } from './migrate.ts';
 import { SCHEMA_SQL } from './schema-embedded.ts';
@@ -17,7 +17,7 @@ import type {
 } from './types.ts';
 import { GBrainError } from './types.ts';
 import * as db from './db.ts';
-import { validateSlug, contentHash, rowToPage, rowToChunk, rowToSearchResult } from './utils.ts';
+import { validateSlug, contentHash, rowToPage, rowToChunk, rowToSearchResult, parseEmbedding } from './utils.ts';
 
 export class PostgresEngine implements BrainEngine {
   private _sql: ReturnType<typeof postgres> | null = null;
@@ -104,7 +104,7 @@ export class PostgresEngine implements BrainEngine {
 
     const rows = await sql`
       INSERT INTO pages (slug, type, title, compiled_truth, timeline, frontmatter, content_hash, updated_at)
-      VALUES (${slug}, ${page.type}, ${page.title}, ${page.compiled_truth}, ${page.timeline || ''}, ${JSON.stringify(frontmatter)}::jsonb, ${hash}, now())
+      VALUES (${slug}, ${page.type}, ${page.title}, ${page.compiled_truth}, ${page.timeline || ''}, ${sql.json(frontmatter)}, ${hash}, now())
       ON CONFLICT (slug) DO UPDATE SET
         type = EXCLUDED.type,
         title = EXCLUDED.title,
@@ -272,7 +272,8 @@ export class PostgresEngine implements BrainEngine {
     `;
     const result = new Map<number, Float32Array>();
     for (const row of rows) {
-      if (row.embedding) result.set(row.id as number, row.embedding as Float32Array);
+      const parsed = parseEmbedding(row.embedding);
+      if (parsed) result.set(row.id as number, parsed);
     }
     return result;
   }
@@ -372,6 +373,30 @@ export class PostgresEngine implements BrainEngine {
     `;
   }
 
+  async addLinksBatch(links: LinkBatchInput[]): Promise<number> {
+    if (links.length === 0) return 0;
+    const sql = this.sql;
+    // unnest() pattern: 4 array-typed bound parameters regardless of batch size.
+    // Avoids the 65535-parameter cap and the postgres-js sql(rows, ...) helper's
+    // identifier-escape gotcha when used inside a (VALUES) subquery.
+    const fromSlugs = links.map(l => l.from_slug);
+    const toSlugs = links.map(l => l.to_slug);
+    // Normalize optional fields to '' to match per-row addLink + NOT NULL DDL.
+    const linkTypes = links.map(l => l.link_type || '');
+    const contexts = links.map(l => l.context || '');
+    const result = await sql`
+      INSERT INTO links (from_page_id, to_page_id, link_type, context)
+      SELECT f.id, t.id, v.link_type, v.context
+      FROM unnest(${fromSlugs}::text[], ${toSlugs}::text[], ${linkTypes}::text[], ${contexts}::text[])
+        AS v(from_slug, to_slug, link_type, context)
+      JOIN pages f ON f.slug = v.from_slug
+      JOIN pages t ON t.slug = v.to_slug
+      ON CONFLICT (from_page_id, to_page_id, link_type) DO NOTHING
+      RETURNING 1
+    `;
+    return result.length;
+  }
+
   async removeLink(from: string, to: string, linkType?: string): Promise<void> {
     const sql = this.sql;
     if (linkType !== undefined) {
@@ -629,6 +654,28 @@ export class PostgresEngine implements BrainEngine {
     `;
   }
 
+  async addTimelineEntriesBatch(entries: TimelineBatchInput[]): Promise<number> {
+    if (entries.length === 0) return 0;
+    const sql = this.sql;
+    // unnest() pattern: 5 array-typed bound parameters regardless of batch size.
+    const slugs = entries.map(e => e.slug);
+    const dates = entries.map(e => e.date);
+    // Normalize optional fields to '' to match per-row addTimelineEntry + NOT NULL DDL.
+    const sources = entries.map(e => e.source || '');
+    const summaries = entries.map(e => e.summary);
+    const details = entries.map(e => e.detail || '');
+    const result = await sql`
+      INSERT INTO timeline_entries (page_id, date, source, summary, detail)
+      SELECT p.id, v.date::date, v.source, v.summary, v.detail
+      FROM unnest(${slugs}::text[], ${dates}::text[], ${sources}::text[], ${summaries}::text[], ${details}::text[])
+        AS v(slug, date, source, summary, detail)
+      JOIN pages p ON p.slug = v.slug
+      ON CONFLICT (page_id, date, summary) DO NOTHING
+      RETURNING 1
+    `;
+    return result.length;
+  }
+
   async getTimeline(slug: string, opts?: TimelineOpts): Promise<TimelineEntry[]> {
     const sql = this.sql;
     const limit = opts?.limit || 100;
@@ -665,7 +712,7 @@ export class PostgresEngine implements BrainEngine {
     const sql = this.sql;
     const result = await sql`
       INSERT INTO raw_data (page_id, source, data)
-      SELECT id, ${source}, ${JSON.stringify(data)}::jsonb
+      SELECT id, ${source}, ${sql.json(data as Record<string, unknown>)}
       FROM pages WHERE slug = ${slug}
       ON CONFLICT (page_id, source) DO UPDATE SET
         data = EXCLUDED.data,
@@ -843,7 +890,7 @@ export class PostgresEngine implements BrainEngine {
     const sql = this.sql;
     await sql`
       INSERT INTO ingest_log (source_type, source_ref, pages_updated, summary)
-      VALUES (${entry.source_type}, ${entry.source_ref}, ${JSON.stringify(entry.pages_updated)}::jsonb, ${entry.summary})
+      VALUES (${entry.source_type}, ${entry.source_ref}, ${sql.json(entry.pages_updated)}, ${entry.summary})
     `;
   }
 
diff --git a/src/core/types.ts b/src/core/types.ts
index cbbf0cca7..4f98ade9f 100644
--- a/src/core/types.ts
+++ b/src/core/types.ts
@@ -1,5 +1,5 @@
 // Page types
-export type PageType = 'person' | 'company' | 'deal' | 'yc' | 'civic' | 'project' | 'concept' | 'source' | 'media';
+export type PageType = 'person' | 'company' | 'deal' | 'yc' | 'civic' | 'project' | 'concept' | 'source' | 'media' | 'writing' | 'analysis' | 'guide' | 'hardware' | 'architecture';
 
 export interface Page {
   id: number;
diff --git a/src/core/utils.ts b/src/core/utils.ts
index 726c5731e..225721218 100644
--- a/src/core/utils.ts
+++ b/src/core/utils.ts
@@ -43,6 +43,51 @@ export function rowToPage(row: Record<string, unknown>): Page {
   };
 }
 
+/**
+ * Normalize an embedding value into a Float32Array.
+ *
+ * pgvector returns embeddings in different shapes depending on driver/path:
+ *   - postgres.js (Postgres): often a string like `"[0.1,0.2,...]"`
+ *   - pglite: typically a numeric array or Float32Array
+ *   - pgvector node binding: numeric array
+ *   - Some queries that JSON-aggregate embeddings: JSON-string array
+ *
+ * Without normalization, downstream cosine math sees a string and produces
+ * NaN scores silently. This helper guarantees a Float32Array or throws
+ * loudly on malformed input — never returns NaN.
+ */
+export function parseEmbedding(value: unknown): Float32Array | null {
+  if (value === null || value === undefined) return null;
+  if (value instanceof Float32Array) return value;
+  if (Array.isArray(value)) {
+    if (value.length === 0) return new Float32Array(0);
+    if (typeof value[0] !== 'number') {
+      throw new Error(`parseEmbedding: array contains non-numeric element (${typeof value[0]})`);
+    }
+    return Float32Array.from(value as number[]);
+  }
+  if (typeof value === 'string') {
+    const trimmed = value.trim();
+    // Plain non-vector strings: treat as "no embedding here", return null.
+    // Strings that LOOK like vector literals but contain garbage: throw,
+    // because that's a real corruption signal worth surfacing loudly.
+    if (!trimmed.startsWith('[') || !trimmed.endsWith(']')) return null;
+    const inner = trimmed.slice(1, -1).trim();
+    if (inner.length === 0) return new Float32Array(0);
+    const parts = inner.split(',');
+    const out = new Float32Array(parts.length);
+    for (let i = 0; i < parts.length; i++) {
+      const n = Number(parts[i].trim());
+      if (!Number.isFinite(n)) {
+        throw new Error(`parseEmbedding: non-finite value at index ${i}: ${parts[i]}`);
+      }
+      out[i] = n;
+    }
+    return out;
+  }
+  return null;
+}
+
 export function rowToChunk(row: Record<string, unknown>, includeEmbedding = false): Chunk {
   return {
     id: row.id as number,
@@ -50,7 +95,7 @@ export function rowToChunk(row: Record<string, unknown>, includeEmbedding = fals
     chunk_index: row.chunk_index as number,
     chunk_text: row.chunk_text as string,
     chunk_source: row.chunk_source as 'compiled_truth' | 'timeline',
-    embedding: includeEmbedding && row.embedding ? row.embedding as Float32Array : null,
+    embedding: includeEmbedding ? parseEmbedding(row.embedding) : null,
     model: row.model as string,
     token_count: row.token_count as number | null,
     embedded_at: row.embedded_at ? new Date(row.embedded_at as string) : null,
diff --git a/test/apply-migrations.test.ts b/test/apply-migrations.test.ts
index 8583f0af7..5d7074be1 100644
--- a/test/apply-migrations.test.ts
+++ b/test/apply-migrations.test.ts
@@ -102,9 +102,10 @@ describe('buildPlan — diff against completed + installed VERSION', () => {
     expect(plan.applied).toEqual([]);
     expect(plan.partial).toEqual([]);
     expect(plan.pending.map(m => m.version)).toContain('0.11.0');
-    // v0.12.0 (Knowledge Graph auto-wire) is registered but installed VERSION
-    // is 0.11.1, so it lands in skippedFuture until the binary catches up.
-    expect(plan.skippedFuture.map(m => m.version)).toEqual(['0.12.0']);
+    // v0.12.0 (Knowledge Graph) and v0.12.2 (JSONB repair) are registered but
+    // installed VERSION is 0.11.1, so they land in skippedFuture until the
+    // binary catches up.
+    expect(plan.skippedFuture.map(m => m.version)).toEqual(['0.12.0', '0.12.2']);
   });
 
   test('already applied → v0.11.0 lands in `applied` bucket, not pending', () => {
@@ -140,7 +141,10 @@ describe('buildPlan — diff against completed + installed VERSION', () => {
     const idx = indexCompleted([]);
     const plan = buildPlan(idx, '0.12.0');
     expect(plan.pending.map(m => m.version)).toContain('0.11.0');
-    expect(plan.skippedFuture).toEqual([]);
+    // v0.12.2 was added later (JSONB repair); installed=0.12.0 means it
+    // belongs in skippedFuture, not pending. v0.11.0 and v0.12.0 stay
+    // pending despite being ≤ installed — that is the H9 invariant.
+    expect(plan.skippedFuture.map(m => m.version)).toEqual(['0.12.2']);
   });
 
   test('--migration filter narrows to one version', () => {
diff --git a/test/e2e/mechanical.test.ts b/test/e2e/mechanical.test.ts
index 0b6175bb9..febc75add 100644
--- a/test/e2e/mechanical.test.ts
+++ b/test/e2e/mechanical.test.ts
@@ -285,6 +285,136 @@ describeE2E('E2E: Timeline', () => {
   });
 });
 
+// ─────────────────────────────────────────────────────────────────
+// Batch methods (addLinksBatch / addTimelineEntriesBatch)
+// ─────────────────────────────────────────────────────────────────
+//
+// Postgres-engine batch methods use postgres-js's sql(rows, 'col1', ...) helper,
+// which is structurally different from PGLite's manual $N placeholder construction
+// (covered in test/pglite-engine.test.ts). These tests verify the postgres-js code
+// path against a real Postgres against the same invariants.
+
+describeE2E('E2E: addLinksBatch (postgres-engine)', () => {
+  beforeAll(async () => {
+    await setupDB();
+    await importFixtures();
+  });
+  afterAll(teardownDB);
+
+  test('empty batch returns 0 with no DB call', async () => {
+    const engine = getEngine();
+    expect(await engine.addLinksBatch([])).toBe(0);
+  });
+
+  test('within-batch duplicates dedup via ON CONFLICT (no 21000 cardinality error)', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    // Deterministic cleanup so re-runs aren't perturbed by prior fixture state.
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-dup'`;
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'people/sarah-chen', to_slug: 'companies/novamind', link_type: 'e2e-batch-dup' },
+      { from_slug: 'people/sarah-chen', to_slug: 'companies/novamind', link_type: 'e2e-batch-dup' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-dup'`;
+  });
+
+  test('rows with missing slug silently dropped by JOIN', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-missing'`;
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'people/does-not-exist', to_slug: 'companies/novamind', link_type: 'e2e-batch-missing' },
+      { from_slug: 'people/sarah-chen', to_slug: 'companies/novamind', link_type: 'e2e-batch-missing' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-missing'`;
+  });
+
+  test('half-existing batch returns count of new only', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-half'`;
+    await engine.addLink('people/sarah-chen', 'companies/novamind', 'pre-existing', 'e2e-batch-half');
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'people/sarah-chen', to_slug: 'companies/novamind', link_type: 'e2e-batch-half' },
+      { from_slug: 'people/sarah-chen', to_slug: 'people/marcus-reid', link_type: 'e2e-batch-half' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM links WHERE link_type = 'e2e-batch-half'`;
+  });
+
+  test('missing optional fields normalize to empty strings (NOT NULL safety)', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM links WHERE link_type = ''`;
+    // No link_type, no context — must default to '' to satisfy NOT NULL.
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'people/sarah-chen', to_slug: 'companies/novamind' },
+    ]);
+    expect(inserted).toBe(1);
+    const rows = await conn`
+      SELECT link_type, context FROM links
+      WHERE from_page_id = (SELECT id FROM pages WHERE slug = 'people/sarah-chen')
+        AND to_page_id = (SELECT id FROM pages WHERE slug = 'companies/novamind')
+        AND link_type = ''
+    `;
+    expect(rows.length).toBe(1);
+    expect(rows[0].context).toBe('');
+    await conn`DELETE FROM links WHERE link_type = ''`;
+  });
+});
+
+describeE2E('E2E: addTimelineEntriesBatch (postgres-engine)', () => {
+  beforeAll(async () => {
+    await setupDB();
+    await importFixtures();
+  });
+  afterAll(teardownDB);
+
+  test('empty batch returns 0', async () => {
+    const engine = getEngine();
+    expect(await engine.addTimelineEntriesBatch([])).toBe(0);
+  });
+
+  test('within-batch duplicates dedup via ON CONFLICT', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM timeline_entries WHERE summary = 'e2e-batch-tl-dup'`;
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'people/sarah-chen', date: '2025-05-01', summary: 'e2e-batch-tl-dup' },
+      { slug: 'people/sarah-chen', date: '2025-05-01', summary: 'e2e-batch-tl-dup' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM timeline_entries WHERE summary = 'e2e-batch-tl-dup'`;
+  });
+
+  test('rows with missing slug silently dropped by JOIN', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM timeline_entries WHERE summary = 'e2e-batch-tl-missing'`;
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'people/no-such-page', date: '2025-05-02', summary: 'e2e-batch-tl-missing' },
+      { slug: 'people/sarah-chen', date: '2025-05-02', summary: 'e2e-batch-tl-missing' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM timeline_entries WHERE summary = 'e2e-batch-tl-missing'`;
+  });
+
+  test('mix of new + existing returns count of new only', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+    await conn`DELETE FROM timeline_entries WHERE summary IN ('e2e-batch-tl-half-1', 'e2e-batch-tl-half-2')`;
+    await engine.addTimelineEntry('people/sarah-chen', { date: '2025-05-03', summary: 'e2e-batch-tl-half-1' });
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'people/sarah-chen', date: '2025-05-03', summary: 'e2e-batch-tl-half-1' },
+      { slug: 'people/sarah-chen', date: '2025-05-04', summary: 'e2e-batch-tl-half-2' },
+    ]);
+    expect(inserted).toBe(1);
+    await conn`DELETE FROM timeline_entries WHERE summary IN ('e2e-batch-tl-half-1', 'e2e-batch-tl-half-2')`;
+  });
+});
+
 // ─────────────────────────────────────────────────────────────────
 // Versions
 // ─────────────────────────────────────────────────────────────────
diff --git a/test/e2e/postgres-jsonb.test.ts b/test/e2e/postgres-jsonb.test.ts
new file mode 100644
index 000000000..ebb694b75
--- /dev/null
+++ b/test/e2e/postgres-jsonb.test.ts
@@ -0,0 +1,174 @@
+/**
+ * E2E JSONB round-trip tests — the test that should have caught the v0.12.0
+ * silent-data-loss bug originally.
+ *
+ * v0.12.0-and-earlier wrote JSONB columns via `${JSON.stringify(value)}::jsonb`
+ * which postgres.js v3 stringified again on the wire. Result: every JSONB
+ * column stored a quoted-string literal instead of an object. Every
+ * `frontmatter->>'key'` query returned NULL. PGLite was unaffected (different
+ * driver path), which is why every previous unit test passed while real
+ * Postgres-backed brains silently lost data.
+ *
+ * These tests exercise each of the four JSONB write sites and assert that:
+ *   1. `jsonb_typeof(col) = 'object'` (or 'array' for array-shaped values)
+ *      — proves the column is a real JSONB structure, not a string literal.
+ *   2. `col->>'key'` returns the expected scalar — proves downstream queries
+ *      and GIN indexes will work as intended.
+ *
+ * Without these E2E assertions, the CI grep guard in scripts/check-jsonb-pattern.sh
+ * is the only protection — and it doesn't catch helper-wrapped or multi-line
+ * variants of the buggy pattern.
+ *
+ * Run: DATABASE_URL=... bun test test/e2e/postgres-jsonb.test.ts
+ */
+
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import {
+  hasDatabase, setupDB, teardownDB, getEngine, getConn,
+} from './helpers.ts';
+
+const skip = !hasDatabase();
+const describeE2E = skip ? describe.skip : describe;
+
+if (skip) {
+  console.log('Skipping E2E JSONB round-trip tests (DATABASE_URL not set)');
+}
+
+describeE2E('Postgres JSONB round-trip — frontmatter / data / pages_updated / metadata', () => {
+  beforeAll(async () => { await setupDB(); });
+  afterAll(async () => { await teardownDB(); });
+
+  test('pages.frontmatter — putPage stores object, not string literal', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+
+    await engine.putPage('jsonb-test/frontmatter', {
+      type: 'concept',
+      title: 'JSONB roundtrip',
+      compiled_truth: 'body',
+      frontmatter: { author: 'garry', score: 7, tags: ['x', 'y'] },
+    });
+
+    const rows = await conn.unsafe(`
+      SELECT
+        jsonb_typeof(frontmatter) AS jt,
+        frontmatter->>'author'    AS author,
+        frontmatter->>'score'     AS score,
+        frontmatter->'tags'       AS tags
+      FROM pages
+      WHERE slug = 'jsonb-test/frontmatter'
+    `);
+
+    expect(rows).toHaveLength(1);
+    expect(rows[0].jt).toBe('object');
+    expect(rows[0].author).toBe('garry');
+    expect(rows[0].score).toBe('7');
+    expect(rows[0].tags).toEqual(['x', 'y']);
+  });
+
+  test('raw_data.data — putRawData stores object, not string literal', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+
+    await engine.putPage('jsonb-test/raw', { type: 'concept', title: 't', compiled_truth: '' });
+    await engine.putRawData('jsonb-test/raw', 'unit-test', { kind: 'fixture', count: 42 });
+
+    const rows = await conn.unsafe(`
+      SELECT
+        jsonb_typeof(rd.data) AS jt,
+        rd.data->>'kind'      AS kind,
+        rd.data->>'count'     AS count
+      FROM raw_data rd
+      JOIN pages p ON p.id = rd.page_id
+      WHERE p.slug = 'jsonb-test/raw' AND rd.source = 'unit-test'
+    `);
+
+    expect(rows).toHaveLength(1);
+    expect(rows[0].jt).toBe('object');
+    expect(rows[0].kind).toBe('fixture');
+    expect(rows[0].count).toBe('42');
+  });
+
+  test('ingest_log.pages_updated — logIngest stores array, not string literal', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+
+    await engine.logIngest({
+      source_type: 'unit-test',
+      source_ref: 'jsonb-roundtrip',
+      pages_updated: ['a/b', 'c/d', 'e/f'],
+      summary: 'roundtrip-check',
+    });
+
+    const rows = await conn.unsafe(`
+      SELECT
+        jsonb_typeof(pages_updated) AS jt,
+        pages_updated->>0           AS first,
+        jsonb_array_length(pages_updated) AS len
+      FROM ingest_log
+      WHERE source_ref = 'jsonb-roundtrip'
+    `);
+
+    expect(rows).toHaveLength(1);
+    expect(rows[0].jt).toBe('array');
+    expect(rows[0].first).toBe('a/b');
+    expect(rows[0].len).toBe(3);
+  });
+
+  test('files.metadata — write site uses sql.json, not string interpolation', async () => {
+    const conn = getConn();
+
+    // Mimic the write at src/commands/files.ts:254 (the bonus fix).
+    await conn`
+      INSERT INTO files (filename, storage_path, mime_type, size_bytes, content_hash, metadata)
+      VALUES (
+        'roundtrip.bin',
+        'unit-test/roundtrip.bin',
+        'application/octet-stream',
+        ${0},
+        'sha256:test',
+        ${conn.json({ type: 'archive', upload_method: 'unit-test' })}
+      )
+    `;
+
+    const rows = await conn.unsafe(`
+      SELECT
+        jsonb_typeof(metadata) AS jt,
+        metadata->>'type'      AS type,
+        metadata->>'upload_method' AS method
+      FROM files
+      WHERE storage_path = 'unit-test/roundtrip.bin'
+    `);
+
+    expect(rows).toHaveLength(1);
+    expect(rows[0].jt).toBe('object');
+    expect(rows[0].type).toBe('archive');
+    expect(rows[0].method).toBe('unit-test');
+  });
+
+  test('page_versions.frontmatter — INSERT...SELECT propagates object shape', async () => {
+    const engine = getEngine();
+    const conn = getConn();
+
+    await engine.putPage('jsonb-test/versioned', {
+      type: 'concept',
+      title: 'versioned',
+      compiled_truth: 'v1',
+      frontmatter: { mood: 'happy' },
+    });
+    await engine.createVersion('jsonb-test/versioned');
+
+    const rows = await conn.unsafe(`
+      SELECT
+        jsonb_typeof(pv.frontmatter) AS jt,
+        pv.frontmatter->>'mood'      AS mood
+      FROM page_versions pv
+      JOIN pages p ON p.id = pv.page_id
+      WHERE p.slug = 'jsonb-test/versioned'
+    `);
+
+    expect(rows.length).toBeGreaterThan(0);
+    expect(rows[0].jt).toBe('object');
+    expect(rows[0].mood).toBe('happy');
+  });
+});
diff --git a/test/extract-fs.test.ts b/test/extract-fs.test.ts
new file mode 100644
index 000000000..ee20e2890
--- /dev/null
+++ b/test/extract-fs.test.ts
@@ -0,0 +1,161 @@
+/**
+ * Tests for `gbrain extract --source fs` (the default, FS-walking path).
+ *
+ * Companion to test/extract-db.test.ts. Specifically guards against the
+ * v0.12.0 N+1 hang: extractLinksFromDir / extractTimelineFromDir used to
+ * pre-load the entire dedup set with one engine.getLinks() per page across
+ * engine.listPages(), which on a 47K-page brain meant 47K sequential
+ * round-trips before any work happened.
+ *
+ * Verifies:
+ *   1. Single run extracts the expected links + timeline entries.
+ *   2. Second run reports `created: 0` (proves DO NOTHING in batch + accurate
+ *      counter via RETURNING).
+ *   3. --dry-run prints the same link found across multiple files exactly
+ *      once (proves the dry-run-only dedup Set works).
+ *   4. Second run wall-clock < 2s (regression guard against any future change
+ *      that re-introduces the N+1 read pre-load).
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach } from 'bun:test';
+import { mkdtempSync, writeFileSync, mkdirSync, rmSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { runExtract } from '../src/commands/extract.ts';
+import type { PageInput } from '../src/core/types.ts';
+
+let engine: PGLiteEngine;
+let brainDir: string;
+
+beforeAll(async () => {
+  engine = new PGLiteEngine();
+  await engine.connect({});
+  await engine.initSchema();
+});
+
+afterAll(async () => {
+  await engine.disconnect();
+});
+
+async function truncateAll() {
+  for (const t of ['content_chunks', 'links', 'tags', 'raw_data', 'timeline_entries', 'page_versions', 'ingest_log', 'pages']) {
+    await (engine as any).db.exec(`DELETE FROM ${t}`);
+  }
+}
+
+const personPage = (title: string, body = ''): PageInput => ({
+  type: 'person', title, compiled_truth: body, timeline: '',
+});
+
+const companyPage = (title: string, body = ''): PageInput => ({
+  type: 'company', title, compiled_truth: body, timeline: '',
+});
+
+beforeEach(async () => {
+  await truncateAll();
+  brainDir = mkdtempSync(join(tmpdir(), 'gbrain-extract-fs-'));
+});
+
+function writeFile(rel: string, content: string) {
+  const full = join(brainDir, rel);
+  mkdirSync(join(full, '..'), { recursive: true });
+  writeFileSync(full, content);
+}
+
+describe('gbrain extract links --source fs', () => {
+  test('first run inserts links, second run reports 0 (idempotent + truthful counter)', async () => {
+    // Set up brain in DB matching the file structure
+    await engine.putPage('people/alice', personPage('Alice'));
+    await engine.putPage('people/bob', personPage('Bob'));
+    await engine.putPage('companies/acme', companyPage('Acme'));
+
+    // Set up matching markdown files on disk
+    writeFile('people/alice.md', '---\ntitle: Alice\n---\n\n[Bob](../people/bob.md) is a friend.\n');
+    writeFile('people/bob.md', '---\ntitle: Bob\n---\n\nWorks at [Acme](../companies/acme.md).\n');
+    writeFile('companies/acme.md', '---\ntitle: Acme\n---\n\nFounded by [Alice](../people/alice.md).\n');
+
+    // First run — write batch path
+    await runExtract(engine, ['links', '--dir', brainDir]);
+    const linksAfter1 = (await engine.getLinks('people/alice'))
+      .concat(await engine.getLinks('people/bob'))
+      .concat(await engine.getLinks('companies/acme'));
+    expect(linksAfter1.length).toBeGreaterThanOrEqual(3);
+
+    // Second run — must dedup via ON CONFLICT and report 0 new (truthful counter)
+    const start = Date.now();
+    await runExtract(engine, ['links', '--dir', brainDir]);
+    const elapsedMs = Date.now() - start;
+
+    const linksAfter2 = (await engine.getLinks('people/alice'))
+      .concat(await engine.getLinks('people/bob'))
+      .concat(await engine.getLinks('companies/acme'));
+    expect(linksAfter2.length).toBe(linksAfter1.length);
+
+    // Perf regression guard: re-run on tiny fixture must not loop through
+    // listPages + per-page getLinks. ~10 files should complete in well under
+    // 2s even on a slow CI box.
+    expect(elapsedMs).toBeLessThan(2000);
+  });
+
+  test('--dry-run dedups duplicate candidates across files (printed once, not N times)', async () => {
+    await engine.putPage('people/alice', personPage('Alice'));
+    await engine.putPage('companies/acme', companyPage('Acme'));
+
+    // Same link target appears in 3 different files. The target file must
+    // exist on disk so the FS extractor's allSlugs Set includes it.
+    writeFile('companies/acme.md', '---\ntitle: Acme\n---\n');
+    writeFile('a.md', '[Acme](companies/acme.md)\n');
+    writeFile('b.md', '[Acme](companies/acme.md)\n');
+    writeFile('c.md', '[Acme](companies/acme.md)\n');
+
+    // Capture stdout to check print frequency
+    const lines: string[] = [];
+    const origLog = console.log;
+    console.log = (...args: unknown[]) => { lines.push(args.join(' ')); };
+    try {
+      await runExtract(engine, ['links', '--dry-run', '--dir', brainDir]);
+    } finally {
+      console.log = origLog;
+    }
+
+    // Each (from, to, link_type) tuple should print at most once.
+    // Three distinct from_slugs (a, b, c) all link to companies/acme, so
+    // we expect 3 link lines (one per source file), not 9.
+    const linkLines = lines.filter(l => l.includes('→') && l.includes('companies/acme'));
+    expect(linkLines.length).toBe(3);
+
+    // No actual writes happened
+    const links = await engine.getLinks('companies/acme');
+    expect(links.length).toBe(0);
+  });
+});
+
+describe('gbrain extract timeline --source fs', () => {
+  test('first run inserts entries, second run reports 0 (idempotent + truthful counter)', async () => {
+    await engine.putPage('people/alice', personPage('Alice'));
+
+    writeFile('people/alice.md', `---
+title: Alice
+---
+
+## Timeline
+
+- **2024-01-15** | source — Founded NovaMind
+- **2024-06-01** | source — Raised seed round
+`);
+
+    await runExtract(engine, ['timeline', '--dir', brainDir]);
+    const after1 = await engine.getTimeline('people/alice');
+    expect(after1.length).toBe(2);
+
+    const start = Date.now();
+    await runExtract(engine, ['timeline', '--dir', brainDir]);
+    const elapsedMs = Date.now() - start;
+
+    const after2 = await engine.getTimeline('people/alice');
+    expect(after2.length).toBe(2);
+
+    expect(elapsedMs).toBeLessThan(2000);
+  });
+});
diff --git a/test/import-file.test.ts b/test/import-file.test.ts
index 60be770a4..c2505f3d8 100644
--- a/test/import-file.test.ts
+++ b/test/import-file.test.ts
@@ -252,7 +252,7 @@ title: Chunked
 
 This is compiled truth content that should be chunked as compiled_truth source.
 
----
+<!-- timeline -->
 
 - 2024-01-01: This is timeline content that should be chunked as timeline source.
 `);
diff --git a/test/markdown.test.ts b/test/markdown.test.ts
index aa2140245..52c468888 100644
--- a/test/markdown.test.ts
+++ b/test/markdown.test.ts
@@ -2,7 +2,7 @@ import { describe, test, expect } from 'bun:test';
 import { parseMarkdown, serializeMarkdown, splitBody } from '../src/core/markdown.ts';
 
 describe('Markdown Parser', () => {
-  test('parses frontmatter + compiled_truth + timeline', () => {
+  test('parses frontmatter + compiled_truth + timeline (explicit sentinel)', () => {
     const md = `---
 type: concept
 title: Do Things That Don't Scale
@@ -11,7 +11,7 @@ tags: [startups, growth]
 
 Paul Graham argues that startups should do unscalable things early on.
 
----
+<!-- timeline -->
 
 - 2013-07-01: Published on paulgraham.com
 - 2024-11-15: Referenced in batch kickoff talk
@@ -90,30 +90,75 @@ Content
 });
 
 describe('splitBody', () => {
-  test('splits at first standalone ---', () => {
-    const body = 'Above the line\n\n---\n\nBelow the line';
+  test('splits at <!-- timeline --> sentinel', () => {
+    const body = 'Above the line\n\n<!-- timeline -->\n\nBelow the line';
     const { compiled_truth, timeline } = splitBody(body);
     expect(compiled_truth).toContain('Above the line');
     expect(timeline).toContain('Below the line');
   });
 
-  test('returns all as compiled_truth if no separator', () => {
+  test('splits at --- timeline --- sentinel', () => {
+    const body = 'Above the line\n\n--- timeline ---\n\nBelow the line';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toContain('Above the line');
+    expect(timeline).toContain('Below the line');
+  });
+
+  test('splits at --- when followed by ## Timeline heading', () => {
+    const body = 'Article content\n\n---\n\n## Timeline\n\n- 2024: Event happened';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toContain('Article content');
+    expect(timeline).toContain('## Timeline');
+    expect(timeline).toContain('Event happened');
+  });
+
+  test('splits at --- when followed by ## History heading', () => {
+    const body = 'Article content\n\n---\n\n## History\n\n- 2020: Founded';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toContain('Article content');
+    expect(timeline).toContain('## History');
+  });
+
+  test('does NOT split at plain --- (horizontal rule in article body)', () => {
+    const body = 'Above the line\n\n---\n\nBelow the line';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toBe(body);
+    expect(timeline).toBe('');
+  });
+
+  test('does NOT split on multiple plain --- horizontal rules', () => {
+    const body = 'Section 1\n\n---\n\nSection 2\n\n---\n\nSection 3';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toBe(body);
+    expect(timeline).toBe('');
+  });
+
+  test('returns all as compiled_truth if no sentinel', () => {
     const body = 'Just some content\nWith multiple lines';
     const { compiled_truth, timeline } = splitBody(body);
     expect(compiled_truth).toBe(body);
     expect(timeline).toBe('');
   });
 
-  test('handles --- at end of content', () => {
+  test('plain --- at end of content stays in compiled_truth', () => {
     const body = 'Content here\n\n---\n';
     const { compiled_truth, timeline } = splitBody(body);
-    expect(compiled_truth).toContain('Content here');
-    expect(timeline.trim()).toBe('');
+    expect(compiled_truth).toBe(body);
+    expect(timeline).toBe('');
+  });
+
+  test('<!-- timeline --> with content before and after', () => {
+    const body = '## Summary\n\nArticle summary here.\n\n---\n\nMore body content.\n\n<!-- timeline -->\n\n- 2024: Timeline entry';
+    const { compiled_truth, timeline } = splitBody(body);
+    expect(compiled_truth).toContain('## Summary');
+    expect(compiled_truth).toContain('More body content.');
+    expect(compiled_truth).not.toContain('Timeline entry');
+    expect(timeline).toContain('Timeline entry');
   });
 });
 
 describe('serializeMarkdown', () => {
-  test('round-trips through parse and serialize', () => {
+  test('round-trips through parse and serialize (explicit sentinel)', () => {
     const original = `---
 type: concept
 title: Do Things That Don't Scale
@@ -125,7 +170,7 @@ custom: value
 
 Paul Graham argues that startups should do unscalable things early on.
 
----
+<!-- timeline -->
 
 - 2013-07-01: Published on paulgraham.com
 `;
@@ -148,7 +193,7 @@ Paul Graham argues that startups should do unscalable things early on.
 });
 
 describe('parseMarkdown edge cases', () => {
-  test('handles content with multiple --- separators', () => {
+  test('does NOT split on plain --- separators (horizontal rules stay in compiled_truth)', () => {
     const md = `---
 type: concept
 title: Test
@@ -158,16 +203,38 @@ First section.
 
 ---
 
-Timeline part 1.
+Second section.
 
 ---
 
-More timeline.`;
+Third section.`;
     const parsed = parseMarkdown(md);
-    // Only splits at the FIRST standalone ---
-    expect(parsed.compiled_truth.trim()).toBe('First section.');
-    expect(parsed.timeline).toContain('Timeline part 1.');
-    expect(parsed.timeline).toContain('More timeline.');
+    expect(parsed.compiled_truth).toContain('First section.');
+    expect(parsed.compiled_truth).toContain('Second section.');
+    expect(parsed.compiled_truth).toContain('Third section.');
+    expect(parsed.timeline).toBe('');
+  });
+
+  test('splits on <!-- timeline --> sentinel with horizontal rules in body', () => {
+    const md = `---
+type: concept
+title: Test
+---
+
+First section.
+
+---
+
+Second section.
+
+<!-- timeline -->
+
+- 2024: Timeline entry`;
+    const parsed = parseMarkdown(md);
+    expect(parsed.compiled_truth).toContain('First section.');
+    expect(parsed.compiled_truth).toContain('Second section.');
+    expect(parsed.compiled_truth).not.toContain('Timeline entry');
+    expect(parsed.timeline).toContain('Timeline entry');
   });
 
   test('handles frontmatter without type or title', () => {
@@ -177,7 +244,7 @@ custom_field: hello
 
 Some content.`;
     const parsed = parseMarkdown(md);
-    expect(parsed.type).toBeTruthy(); // should have a default
+    expect(parsed.type).toBeTruthy();
     expect(parsed.compiled_truth.trim()).toBe('Some content.');
     expect(parsed.frontmatter.custom_field).toBe('hello');
   });
@@ -199,4 +266,19 @@ Some content.`;
     expect(parseMarkdown('', 'concepts/thing.md').type).toBe('concept');
     expect(parseMarkdown('', 'companies/acme.md').type).toBe('company');
   });
+
+  test('infers type from wiki subdirectory paths', () => {
+    expect(parseMarkdown('', 'tech/wiki/concepts/longevity-science.md').type).toBe('concept');
+    expect(parseMarkdown('', 'tech/wiki/guides/team-os-claude-code.md').type).toBe('guide');
+    expect(parseMarkdown('', 'tech/wiki/analysis/agi-timeline-debate.md').type).toBe('analysis');
+    expect(parseMarkdown('', 'tech/wiki/hardware/h100-vs-gb200-training-benchmarks.md').type).toBe('hardware');
+    expect(parseMarkdown('', 'tech/wiki/architecture/kb-infrastructure.md').type).toBe('architecture');
+    expect(parseMarkdown('', 'finance/wiki/analysis/polymarket-bot-automation-thesis.md').type).toBe('analysis');
+    expect(parseMarkdown('', 'personal/wiki/concepts/career-regrets-2026-framework.md').type).toBe('concept');
+  });
+
+  test('infers writing type from /writing/ paths', () => {
+    expect(parseMarkdown('', 'writing/post.md').type).toBe('writing');
+    expect(parseMarkdown('', 'projects/blog/writing/essay.md').type).toBe('writing');
+  });
 });
diff --git a/test/migrate.test.ts b/test/migrate.test.ts
index c569dd07f..ed106f147 100644
--- a/test/migrate.test.ts
+++ b/test/migrate.test.ts
@@ -1,5 +1,6 @@
-import { describe, test, expect } from 'bun:test';
-import { LATEST_VERSION } from '../src/core/migrate.ts';
+import { describe, test, expect, beforeAll, afterAll } from 'bun:test';
+import { LATEST_VERSION, runMigrations, MIGRATIONS } from '../src/core/migrate.ts';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
 
 describe('migrate', () => {
   test('LATEST_VERSION is a number >= 1', () => {
@@ -8,10 +9,192 @@ describe('migrate', () => {
   });
 
   test('runMigrations is exported and callable', async () => {
-    const { runMigrations } = await import('../src/core/migrate.ts');
     expect(typeof runMigrations).toBe('function');
   });
 
   // Integration tests for actual migration execution require DATABASE_URL
   // and are covered in the E2E suite (test/e2e/mechanical.test.ts)
 });
+
+// ─────────────────────────────────────────────────────────────────
+// REGRESSION TESTS — migrations v8 + v9 perf on duplicate-heavy tables
+// ─────────────────────────────────────────────────────────────────
+//
+// Garry's production brain hit Supabase Management API's 60s ceiling because
+// the DELETE...USING self-join in migrations v8 + v9 was O(n²) without an
+// index on the dedup columns. The fix pre-creates a btree helper index
+// before the DELETE, then drops it. These tests guard against any future
+// change that re-introduces the missing helper index.
+//
+// Two-layer guard:
+//   1. Structural — assert the migration SQL literally contains the helper
+//      CREATE INDEX + DROP INDEX (deterministic, fast, catches the regression
+//      even at 0-row scale where wall-clock can't distinguish O(n²) from O(1)).
+//   2. Behavioral — populate 1000 duplicates and assert the migration completes
+//      under the wall-clock cap. Sanity check at small scale; the structural
+//      assertion is the real guard.
+
+describe('migrations v8 + v9 — structural guard for helper-index fix', () => {
+  test('migration v8 SQL contains idx_links_dedup_helper CREATE+DROP around the DELETE', () => {
+    const v8 = MIGRATIONS.find(m => m.version === 8);
+    expect(v8).toBeDefined();
+    const sql = v8!.sql;
+
+    // The fix must: (a) create the helper btree, (b) DELETE...USING, (c) drop the helper, (d) add the unique constraint.
+    // If anyone reorders or removes the helper-index lines, this fails.
+    expect(sql).toContain('CREATE INDEX IF NOT EXISTS idx_links_dedup_helper');
+    expect(sql).toContain('ON links(from_page_id, to_page_id, link_type)');
+    expect(sql).toContain('DROP INDEX IF EXISTS idx_links_dedup_helper');
+    expect(sql).toContain('DELETE FROM links a USING links b');
+    expect(sql).toContain('ALTER TABLE links ADD CONSTRAINT links_from_to_type_unique');
+
+    // Order matters: CREATE INDEX before DELETE, DROP INDEX after DELETE, before ADD CONSTRAINT.
+    const createIdx = sql.indexOf('CREATE INDEX IF NOT EXISTS idx_links_dedup_helper');
+    const deleteUsing = sql.indexOf('DELETE FROM links a USING links b');
+    const dropIdx = sql.indexOf('DROP INDEX IF EXISTS idx_links_dedup_helper');
+    const addConstraint = sql.indexOf('ALTER TABLE links ADD CONSTRAINT links_from_to_type_unique');
+    expect(createIdx).toBeLessThan(deleteUsing);
+    expect(deleteUsing).toBeLessThan(dropIdx);
+    expect(dropIdx).toBeLessThan(addConstraint);
+  });
+
+  test('migration v9 SQL contains idx_timeline_dedup_helper CREATE+DROP around the DELETE', () => {
+    const v9 = MIGRATIONS.find(m => m.version === 9);
+    expect(v9).toBeDefined();
+    const sql = v9!.sql;
+
+    expect(sql).toContain('CREATE INDEX IF NOT EXISTS idx_timeline_dedup_helper');
+    expect(sql).toContain('ON timeline_entries(page_id, date, summary)');
+    expect(sql).toContain('DROP INDEX IF EXISTS idx_timeline_dedup_helper');
+    expect(sql).toContain('DELETE FROM timeline_entries a USING timeline_entries b');
+    expect(sql).toContain('CREATE UNIQUE INDEX IF NOT EXISTS idx_timeline_dedup');
+
+    const createHelper = sql.indexOf('CREATE INDEX IF NOT EXISTS idx_timeline_dedup_helper');
+    const deleteUsing = sql.indexOf('DELETE FROM timeline_entries a USING timeline_entries b');
+    const dropHelper = sql.indexOf('DROP INDEX IF EXISTS idx_timeline_dedup_helper');
+    const createUnique = sql.indexOf('CREATE UNIQUE INDEX IF NOT EXISTS idx_timeline_dedup');
+    expect(createHelper).toBeLessThan(deleteUsing);
+    expect(deleteUsing).toBeLessThan(dropHelper);
+    expect(dropHelper).toBeLessThan(createUnique);
+  });
+});
+
+describe('migrate: v8 (links_dedup) regression — must be fast on 1K duplicate rows', () => {
+  let engine: PGLiteEngine;
+
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+  });
+
+  afterAll(async () => {
+    await engine.disconnect();
+  });
+
+  test('1000 duplicate links dedup completes in <5s and leaves table deduped', async () => {
+    // Set up: drop the unique constraint so duplicates can be inserted, then reset
+    // version so v8 re-runs. Schema-embedded.ts already has the constraint, so
+    // initSchema() above set it up; explicit DROP makes the test premise valid.
+    const db = (engine as any).db;
+    await db.exec(`ALTER TABLE links DROP CONSTRAINT IF EXISTS links_from_to_type_unique`);
+
+    // Two pages so the FK is satisfied
+    await engine.putPage('p/from', { type: 'concept', title: 'F', compiled_truth: '', timeline: '' });
+    await engine.putPage('p/to', { type: 'concept', title: 'T', compiled_truth: '', timeline: '' });
+    const fromId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/from'`)).rows[0].id;
+    const toId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/to'`)).rows[0].id;
+
+    // Insert 1000 duplicates of the same (from, to, type) row
+    for (let i = 0; i < 1000; i++) {
+      await db.query(
+        `INSERT INTO links (from_page_id, to_page_id, link_type, context) VALUES ($1, $2, $3, $4)`,
+        [fromId, toId, 'mention', `dup-${i}`]
+      );
+    }
+    const beforeCount = (await db.query(`SELECT COUNT(*)::int AS c FROM links`)).rows[0].c;
+    expect(beforeCount).toBe(1000);
+
+    // Reset version to 7 so v8 + v9 + v10 re-run
+    await engine.setConfig('version', '7');
+
+    // Run migrations and assert wall-clock + correctness
+    const start = Date.now();
+    await runMigrations(engine);
+    const elapsedMs = Date.now() - start;
+
+    expect(elapsedMs).toBeLessThan(5000);
+
+    const afterCount = (await db.query(`SELECT COUNT(*)::int AS c FROM links`)).rows[0].c;
+    expect(afterCount).toBe(1); // deduped to one row
+
+    // Unique constraint reinstated
+    const constraints = (await db.query(`
+      SELECT conname FROM pg_constraint
+      WHERE conrelid = 'links'::regclass AND contype = 'u'
+    `)).rows;
+    expect(constraints.some((c: { conname: string }) => c.conname === 'links_from_to_type_unique')).toBe(true);
+
+    // Helper index was dropped after dedup
+    const helperIdx = (await db.query(`
+      SELECT indexname FROM pg_indexes
+      WHERE tablename = 'links' AND indexname = 'idx_links_dedup_helper'
+    `)).rows;
+    expect(helperIdx.length).toBe(0);
+  });
+});
+
+describe('migrate: v9 (timeline_dedup_index) regression — must be fast on 1K duplicate rows', () => {
+  let engine: PGLiteEngine;
+
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+  });
+
+  afterAll(async () => {
+    await engine.disconnect();
+  });
+
+  test('1000 duplicate timeline entries dedup completes in <5s and leaves table deduped', async () => {
+    const db = (engine as any).db;
+    await db.exec(`DROP INDEX IF EXISTS idx_timeline_dedup`);
+
+    await engine.putPage('p/timeline', { type: 'concept', title: 'TL', compiled_truth: '', timeline: '' });
+    const pageId = (await db.query(`SELECT id FROM pages WHERE slug = 'p/timeline'`)).rows[0].id;
+
+    // Insert 1000 duplicates of the same (page_id, date, summary) row
+    for (let i = 0; i < 1000; i++) {
+      await db.query(
+        `INSERT INTO timeline_entries (page_id, date, source, summary, detail) VALUES ($1, $2::date, $3, $4, $5)`,
+        [pageId, '2024-01-15', `src-${i}`, 'Founded NovaMind', `detail-${i}`]
+      );
+    }
+    const beforeCount = (await db.query(`SELECT COUNT(*)::int AS c FROM timeline_entries`)).rows[0].c;
+    expect(beforeCount).toBe(1000);
+
+    await engine.setConfig('version', '7');
+
+    const start = Date.now();
+    await runMigrations(engine);
+    const elapsedMs = Date.now() - start;
+
+    expect(elapsedMs).toBeLessThan(5000);
+
+    const afterCount = (await db.query(`SELECT COUNT(*)::int AS c FROM timeline_entries`)).rows[0].c;
+    expect(afterCount).toBe(1);
+
+    const uniqueIdx = (await db.query(`
+      SELECT indexname FROM pg_indexes
+      WHERE tablename = 'timeline_entries' AND indexname = 'idx_timeline_dedup'
+    `)).rows;
+    expect(uniqueIdx.length).toBe(1);
+
+    const helperIdx = (await db.query(`
+      SELECT indexname FROM pg_indexes
+      WHERE tablename = 'timeline_entries' AND indexname = 'idx_timeline_dedup_helper'
+    `)).rows;
+    expect(helperIdx.length).toBe(0);
+  });
+});
diff --git a/test/migrations-v0_12_2.test.ts b/test/migrations-v0_12_2.test.ts
new file mode 100644
index 000000000..14e616318
--- /dev/null
+++ b/test/migrations-v0_12_2.test.ts
@@ -0,0 +1,59 @@
+/**
+ * Tests for the v0.12.2 JSONB-double-encode-repair orchestrator.
+ *
+ * Covers the contract that makes this migration safe to ship:
+ *   - Registered in the TS registry (so apply-migrations sees it).
+ *   - Phase functions exported via __testing for unit-level coverage.
+ *   - Dry-run skips all side-effect phases.
+ *   - Feature pitch explains what the user can NOW do that they couldn't.
+ *
+ * Idempotency, repair correctness, and PGLite-no-op behavior are exercised
+ * end-to-end against real Postgres in test/e2e/postgres-jsonb.test.ts.
+ */
+
+import { describe, test, expect } from 'bun:test';
+
+describe('v0.12.2 — JSONB double-encode repair migration', () => {
+  test('registered in the TS migration registry', async () => {
+    const { migrations, getMigration } = await import('../src/commands/migrations/index.ts');
+    const versions = migrations.map(m => m.version);
+    expect(versions).toContain('0.12.2');
+    const m = getMigration('0.12.2');
+    expect(m).not.toBeNull();
+    expect(m!.featurePitch.headline).toContain('JSONB');
+    expect(typeof m!.orchestrator).toBe('function');
+  });
+
+  test('feature pitch lists the affected columns and the recovery path', async () => {
+    const { v0_12_2 } = await import('../src/commands/migrations/v0_12_2.ts');
+    const desc = v0_12_2.featurePitch.description ?? '';
+    expect(desc).toContain('pages.frontmatter');
+    expect(desc).toContain('raw_data.data');
+    expect(desc).toContain('ingest_log.pages_updated');
+    expect(desc).toContain('files.metadata');
+    expect(desc).toContain('page_versions.frontmatter');
+    expect(desc).toContain('gbrain sync --full');
+  });
+
+  test('phase functions exported for unit testing', async () => {
+    const { __testing } = await import('../src/commands/migrations/v0_12_2.ts');
+    expect(typeof __testing.phaseASchema).toBe('function');
+    expect(typeof __testing.phaseBRepair).toBe('function');
+    expect(typeof __testing.phaseCVerify).toBe('function');
+  });
+
+  test('dry-run skips all side-effect phases', async () => {
+    const { v0_12_2 } = await import('../src/commands/migrations/v0_12_2.ts');
+    const result = await v0_12_2.orchestrator({
+      yes: true,
+      dryRun: true,
+      noAutopilotInstall: true,
+    });
+    expect(result.version).toBe('0.12.2');
+    expect(result.phases.length).toBeGreaterThanOrEqual(3);
+    for (const p of result.phases) {
+      expect(p.status).toBe('skipped');
+      expect(p.detail).toContain('dry-run');
+    }
+  });
+});
diff --git a/test/pglite-engine.test.ts b/test/pglite-engine.test.ts
index 130821558..b2e09576a 100644
--- a/test/pglite-engine.test.ts
+++ b/test/pglite-engine.test.ts
@@ -350,6 +350,118 @@ describe('PGLiteEngine: Timeline', () => {
   });
 });
 
+// ─────────────────────────────────────────────────────────────────
+// Batch methods (addLinksBatch / addTimelineEntriesBatch)
+// ─────────────────────────────────────────────────────────────────
+describe('PGLiteEngine: addLinksBatch', () => {
+  beforeEach(async () => {
+    await truncateAll();
+    await engine.putPage('a', { type: 'concept', title: 'A', compiled_truth: '', timeline: '' });
+    await engine.putPage('b', { type: 'concept', title: 'B', compiled_truth: '', timeline: '' });
+    await engine.putPage('c', { type: 'concept', title: 'C', compiled_truth: '', timeline: '' });
+  });
+
+  test('empty batch returns 0 with no DB call', async () => {
+    expect(await engine.addLinksBatch([])).toBe(0);
+  });
+
+  test('batch of 1 with missing optional fields inserts row with empty defaults', async () => {
+    const inserted = await engine.addLinksBatch([{ from_slug: 'a', to_slug: 'b' }]);
+    expect(inserted).toBe(1);
+    const links = await engine.getLinks('a');
+    expect(links.length).toBe(1);
+    expect(links[0].context).toBe('');
+    expect(links[0].link_type).toBe('');
+  });
+
+  test('within-batch duplicates are deduped via ON CONFLICT (no 21000 error)', async () => {
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'a', to_slug: 'b', link_type: 'mention' },
+      { from_slug: 'a', to_slug: 'b', link_type: 'mention' },
+      { from_slug: 'a', to_slug: 'c', link_type: 'mention' },
+    ]);
+    expect(inserted).toBe(2);
+  });
+
+  test('rows with missing slug are silently dropped by JOIN', async () => {
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'doesnt-exist', to_slug: 'b' },
+      { from_slug: 'a', to_slug: 'b' },
+    ]);
+    expect(inserted).toBe(1);
+  });
+
+  test('half-existing batch returns count of new only', async () => {
+    await engine.addLink('a', 'b', '', 'mention');
+    const inserted = await engine.addLinksBatch([
+      { from_slug: 'a', to_slug: 'b', link_type: 'mention' },
+      { from_slug: 'a', to_slug: 'c', link_type: 'mention' },
+    ]);
+    expect(inserted).toBe(1);
+  });
+
+  test('batch of 100 fresh rows returns 100', async () => {
+    // Create 100 target pages
+    for (let i = 0; i < 100; i++) {
+      await engine.putPage(`target/${i}`, { type: 'concept', title: `T${i}`, compiled_truth: '', timeline: '' });
+    }
+    const batch = Array.from({ length: 100 }, (_, i) => ({
+      from_slug: 'a', to_slug: `target/${i}`, link_type: 'mention',
+    }));
+    expect(await engine.addLinksBatch(batch)).toBe(100);
+  });
+});
+
+describe('PGLiteEngine: addTimelineEntriesBatch', () => {
+  beforeEach(async () => {
+    await truncateAll();
+    await engine.putPage('p1', { type: 'concept', title: 'P1', compiled_truth: '', timeline: '' });
+    await engine.putPage('p2', { type: 'concept', title: 'P2', compiled_truth: '', timeline: '' });
+  });
+
+  test('empty batch returns 0', async () => {
+    expect(await engine.addTimelineEntriesBatch([])).toBe(0);
+  });
+
+  test('batch of 1 with missing optionals inserts with empty defaults', async () => {
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'p1', date: '2024-01-15', summary: 'Founded' },
+    ]);
+    expect(inserted).toBe(1);
+    const entries = await engine.getTimeline('p1');
+    expect(entries.length).toBe(1);
+    expect(entries[0].source).toBe('');
+    expect(entries[0].detail).toBe('');
+  });
+
+  test('within-batch duplicates are deduped via ON CONFLICT', async () => {
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'p1', date: '2024-01-15', summary: 'Founded' },
+      { slug: 'p1', date: '2024-01-15', summary: 'Founded' },
+      { slug: 'p1', date: '2024-02-01', summary: 'Launched' },
+    ]);
+    expect(inserted).toBe(2);
+  });
+
+  test('rows with missing slug are silently dropped by JOIN', async () => {
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'no-such-page', date: '2024-01-15', summary: 'Phantom' },
+      { slug: 'p1', date: '2024-01-15', summary: 'Real' },
+    ]);
+    expect(inserted).toBe(1);
+  });
+
+  test('mix of new + existing returns count of new only', async () => {
+    await engine.addTimelineEntry('p1', { date: '2024-01-15', summary: 'Founded' });
+    const inserted = await engine.addTimelineEntriesBatch([
+      { slug: 'p1', date: '2024-01-15', summary: 'Founded' },
+      { slug: 'p1', date: '2024-02-01', summary: 'Launched' },
+      { slug: 'p2', date: '2024-03-01', summary: 'Spun off' },
+    ]);
+    expect(inserted).toBe(2);
+  });
+});
+
 // ─────────────────────────────────────────────────────────────────
 // Raw Data, Versions, Config, IngestLog
 // ─────────────────────────────────────────────────────────────────
diff --git a/test/repair-jsonb.test.ts b/test/repair-jsonb.test.ts
new file mode 100644
index 000000000..6b774e4e3
--- /dev/null
+++ b/test/repair-jsonb.test.ts
@@ -0,0 +1,37 @@
+/**
+ * Unit tests for `gbrain repair-jsonb`.
+ *
+ * The actual repair logic runs against real Postgres in
+ * test/e2e/postgres-jsonb.test.ts (covers the round-trip + the migration
+ * orchestrator end to end). Here we cover only the engine-detection
+ * short-circuit: PGLite was never affected by the JSONB double-encode bug,
+ * so the command must report 0 repaired rows and never connect.
+ */
+
+import { describe, test, expect } from 'bun:test';
+import { repairJsonb } from '../src/commands/repair-jsonb.ts';
+
+describe('repairJsonb — PGLite short-circuit', () => {
+  test('PGLite engines short-circuit: no DB connection, all targets report 0 repaired', async () => {
+    const result = await repairJsonb({
+      dryRun: false,
+      engineConfig: { engine: 'pglite' },
+    });
+    expect(result.engine).toBe('pglite');
+    expect(result.total_repaired).toBe(0);
+    // All 5 columns reported: pages.frontmatter, raw_data.data,
+    // ingest_log.pages_updated, files.metadata, page_versions.frontmatter.
+    expect(result.per_target.length).toBe(5);
+    for (const t of result.per_target) {
+      expect(t.rows_repaired).toBe(0);
+    }
+    const tables = result.per_target.map(t => `${t.table}.${t.column}`).sort();
+    expect(tables).toEqual([
+      'files.metadata',
+      'ingest_log.pages_updated',
+      'page_versions.frontmatter',
+      'pages.frontmatter',
+      'raw_data.data',
+    ]);
+  });
+});
diff --git a/test/utils.test.ts b/test/utils.test.ts
index c11d57257..da80dcb3d 100644
--- a/test/utils.test.ts
+++ b/test/utils.test.ts
@@ -1,5 +1,5 @@
 import { describe, test, expect } from 'bun:test';
-import { validateSlug, contentHash, rowToPage, rowToChunk, rowToSearchResult } from '../src/core/utils.ts';
+import { validateSlug, contentHash, parseEmbedding, rowToPage, rowToChunk, rowToSearchResult } from '../src/core/utils.ts';
 
 describe('validateSlug', () => {
   test('accepts valid slugs', () => {
@@ -98,6 +98,52 @@ describe('rowToChunk', () => {
     }, true);
     expect(chunk.embedding).not.toBeNull();
   });
+
+  test('parses pgvector string embeddings when requested', () => {
+    const chunk = rowToChunk({
+      id: 1, page_id: 1, chunk_index: 0, chunk_text: 'text',
+      chunk_source: 'compiled_truth', embedding: '[0.1, 0.2, 0.3]',
+      model: 'test', token_count: 5, embedded_at: '2024-01-01',
+    }, true);
+    expect(chunk.embedding).toBeInstanceOf(Float32Array);
+    expect(Array.from(chunk.embedding || [])).toHaveLength(3);
+    expect(chunk.embedding?.[0]).toBeCloseTo(0.1, 6);
+    expect(chunk.embedding?.[1]).toBeCloseTo(0.2, 6);
+    expect(chunk.embedding?.[2]).toBeCloseTo(0.3, 6);
+  });
+});
+
+describe('parseEmbedding', () => {
+  test('returns Float32Array unchanged', () => {
+    const emb = new Float32Array([0.1, 0.2]);
+    expect(parseEmbedding(emb)).toBe(emb);
+  });
+
+  test('parses pgvector text into Float32Array', () => {
+    const parsed = parseEmbedding('[0.1, 0.2, 0.3]');
+    expect(parsed).toBeInstanceOf(Float32Array);
+    expect(Array.from(parsed || [])).toHaveLength(3);
+    expect(parsed?.[0]).toBeCloseTo(0.1, 6);
+    expect(parsed?.[1]).toBeCloseTo(0.2, 6);
+    expect(parsed?.[2]).toBeCloseTo(0.3, 6);
+  });
+
+  test('returns null for unsupported embedding values', () => {
+    expect(parseEmbedding(null)).toBeNull();
+    expect(parseEmbedding(undefined)).toBeNull();
+    expect(parseEmbedding('not-a-vector')).toBeNull();
+  });
+
+  test('parses numeric array into Float32Array', () => {
+    const parsed = parseEmbedding([0.5, 0.25, 0.125]);
+    expect(parsed).toBeInstanceOf(Float32Array);
+    expect(parsed?.[0]).toBeCloseTo(0.5, 6);
+  });
+
+  test('throws on vector-like string with non-numeric content (no silent NaN)', () => {
+    expect(() => parseEmbedding('[abc, def]')).toThrow();
+    expect(() => parseEmbedding('[1, NaN, 3]')).toThrow();
+  });
 });
 
 describe('rowToSearchResult', () => {