fix: JSONB double-encode + splitBody wiki + parseEmbedding (v0.12.1) (#196)

* fix: splitBody and inferType for wiki-style markdown content

- splitBody now requires explicit timeline sentinel (<!-- timeline -->,
  --- timeline ---, or --- directly before ## Timeline / ## History).
  A bare --- in body text is a markdown horizontal rule, not a separator.
  This fixes the 83% content truncation @knee5 reported on a 1,991-article
  wiki where 4,856 of 6,680 wikilinks were lost.

- serializeMarkdown emits <!-- timeline --> sentinel for round-trip stability.

- inferType extended with /writing/, /wiki/analysis/, /wiki/guides/,
  /wiki/hardware/, /wiki/architecture/, /wiki/concepts/. Path order is
  most-specific-first so projects/blog/writing/essay.md → writing,
  not project.

- PageType union extended: writing, analysis, guide, hardware, architecture.

Updates test/import-file.test.ts to use the new sentinel.

Co-Authored-By: @knee5 (PR #187)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* fix: JSONB double-encode bug on Postgres + parseEmbedding NaN scores

Two related Postgres-string-typed-data bugs that PGLite hid:

1. JSONB double-encode (postgres-engine.ts:107,668,846 + files.ts:254):
   ${JSON.stringify(value)}::jsonb in postgres.js v3 stringified again
   on the wire, storing JSONB columns as quoted string literals. Every
   frontmatter->>'key' returned NULL on Postgres-backed brains; GIN
   indexes were inert. Switched to sql.json(value), which is the
   postgres.js-native JSONB encoder (Parameter with OID 3802).
   Affected columns: pages.frontmatter, raw_data.data,
   ingest_log.pages_updated, files.metadata. page_versions.frontmatter
   is downstream via INSERT...SELECT and propagates the fix.

2. pgvector embeddings returning as strings (utils.ts):
   getEmbeddingsByChunkIds returned "[0.1,0.2,...]" instead of
   Float32Array on Supabase, producing [NaN] cosine scores.
   Adds parseEmbedding() helper handling Float32Array, numeric arrays,
   and pgvector string format. Throws loud on malformed vectors
   (per Codex's no-silent-NaN requirement); returns null for
   non-vector strings (treated as "no embedding here"). rowToChunk
   delegates to parseEmbedding.

E2E regression test at test/e2e/postgres-jsonb.test.ts asserts
jsonb_typeof = 'object' AND col->>'k' returns expected scalar across
all 5 affected columns — the test that should have caught the original
bug. Runs in CI via the existing pgvector service.

Co-Authored-By: @knee5 (PR #187 — JSONB triple-fix)
Co-Authored-By: @leonardsellem (PR #175 — parseEmbedding)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: extract wikilink syntax with ancestor-search slug resolution

extractMarkdownLinks now handles [[page]] and [[page|Display Text]]
alongside standard [text](page.md). For wiki KBs where authors omit
leading ../ (thinking in wiki-root-relative terms), resolveSlug
walks ancestor directories until it finds a matching slug.

Without this, wikilinks under tech/wiki/analysis/ targeting
[[../../finance/wiki/concepts/foo]] silently dangled when the
correct relative depth was 3 × ../ instead of 2.

Co-Authored-By: @knee5 (PR #187)
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* feat: gbrain repair-jsonb + v0.12.1 migration + CI grep guard

- New gbrain repair-jsonb command. Detects rows where
  jsonb_typeof(col) = 'string' and rewrites them via
  (col #>> '{}')::jsonb across 5 affected columns:
  pages.frontmatter, raw_data.data, ingest_log.pages_updated,
  files.metadata, page_versions.frontmatter. Idempotent — re-running
  is a no-op. PGLite engines short-circuit cleanly (the bug never
  affected the parameterized encode path PGLite uses). --dry-run
  shows what would be repaired; --json for scripting.

- New v0_12_1.ts migration orchestrator. Phases: schema → repair → verify.
  Modeled on v0_12_0 pattern, registered in migrations/index.ts.
  Runs automatically via gbrain upgrade / apply-migrations.

- 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 via package.json. Best-effort static
  analysis (multi-line and helper-wrapped variants are caught by the
  E2E round-trip test instead).

- Updates apply-migrations.test.ts expectations to account for the new
  v0.12.1 entry in the registry.

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

* chore: bump version and changelog (v0.12.1)

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

* docs: update project documentation for v0.12.1

- CLAUDE.md: document repair-jsonb command, v0_12_1 migration,
  splitBody sentinel contract, inferType wiki subtypes, CI grep
  guard, new test files (repair-jsonb, migrations-v0_12_1, markdown)
- README.md: add gbrain repair-jsonb to ADMIN command reference
- INSTALL_FOR_AGENTS.md: fix verification count (6 -> 7), add
  v0.12.1 upgrade guidance for Postgres brains
- docs/GBRAIN_VERIFY.md: add check #8 for JSONB integrity on
  Postgres-backed brains
- docs/UPGRADING_DOWNSTREAM_AGENTS.md: add v0.12.1 section with
  migration steps, splitBody contract, wiki subtype inference
- skills/migrate/SKILL.md: document native wikilink extraction
  via gbrain extract links (v0.12.1+)

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

---------

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

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.