os.Root refuses links that leave the brain on its own, so the slice 1-3
callers' outside-target tests stayed green when a caller read without
brainfs's Lstat/SameFile checks (PR #168 round-2 review). Adds a static
in-brain link (wiki/w/facts/inlink.md -> ../../../raw/s.md) and an
AssertNoLeakFrom swap race with an in-brain target for search.Query,
hydrate, vectorstore.Sync, readExcerpt and api.ReadNote.
Flip-verified: replacing each caller's bfs.ReadRegular with an
os.OpenRoot(brainDir).ReadFile turns every one red on the new assertions
(Query, hydrate, Sync, readExcerpt, ReadNote).
Also from that review: rename TestReadRegularNever... to
...DoesNotReturn... (rule 9: a sampled race), and AssertNoLeakFrom's
failure message names the symlink target instead of 'outside file'.
Closes#171
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
vectorstore.Sync walks and reads via brainfs (regular files only, handle-checked), so symlinked notes are no longer embedded and their old chunks are purged. brainfs.WalkRegular requires every component of its root to be a real directory (fixes in-brain root aliasing in Sync and search Wing/Wing+Hall). Walk errors, including a symlinked scan root, abort Sync before the delete pass. brainfs gains Lstat. Directory-swap race recorded as accepted residual (#167).
Refs #157. Adversarial review: BLOCKED, BLOCKED, PASS.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
Estate-wide consolidation pass. golangci-lint v2 default set enables NO
formatter, so gofmt drift accumulated silently across the estate -- 8 repos
were carrying it, this one included. Same hole that let two files rot in
dma-cli until they were found by hand (dma-cli#12).
Mechanical and deterministic: `gofmt -w`, nothing hand-edited. Verified
before commit -- gofmt -l now reports 0, go build and go vet both pass.
Clears this repo to adopt the canonical .golangci.yml (infra
ci-templates/golangci.yml, infra#309 pattern) in a later wave.
A doc with no headings and no blank-line paragraphs (JSON-lines, e.g.
wiki/telos/decisions/human-intent-column.md) survived both chunk passes whole
and was sent to nomic-embed over its context window → 'input length exceeds
the context length' (400, the steady embed errors=1). Add a final hard-split
pass (line then UTF-8 rune boundaries) so no chunk exceeds maxBytes. TDD.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Removes the TODO in Sync that left files static after their first embed.
Edits to brain/wiki/ and brain/knowledge/ now surface in subsequent
syncs without manual /backfill-embeddings calls.
Approach
- Store interface: KnownPaths → KnownPathsWithTime returning path →
updated_at. Callers compare against file mtime to detect edits.
- PGStore: SELECT path, updated_at FROM brain_embeddings.
- Sync groups known chunks by parent path and tracks the EARLIEST
updated_at per parent. A file is stale when its mtime is after that
oldest chunk's timestamp — any chunk older than the file means at
least one chunk hasn't been refreshed since the last edit.
- Stale-path rewrite: delete every old chunk for the parent (handles
"file shrunk → fewer chunks → orphan rows at higher #NNNN" cleanly),
then re-chunk + re-embed + re-upsert.
Tests
- New: TestSync_ReembedsFileWhenMtimeNewer — file mtime forced into the
future vs store updated_at; Sync deletes old chunk + upserts fresh one.
- New: TestSync_SkipsFileWhenMtimeOlder — file mtime backdated; Sync is
a no-op (no upserts, no deletes).
- Updated: stubStore.known is now map[string]time.Time. A zero value
resolves to a far-future sentinel so existing "skip if already known"
tests keep passing without per-test setup.
- pg_test renamed KnownPaths integration → KnownPathsWithTime; asserts
updated_at is non-zero and within 5s of insert wall-clock.
Backward compat
- brain_embeddings rows pre-dating this change carry valid updated_at
values (column was always populated via `DEFAULT now()` + ON CONFLICT
`updated_at = now()`). No migration needed. Live pod will start
re-embedding any file whose source has been edited since its chunks
were originally written.
Closes gitea/mathias/hyperguild#23.
Long markdown files (>~8KB) silently failed to embed because nomic-embed-text
on iguana has a 2048-token context. embed sync logged errors=1 every cycle
with no useful body until #37 added per-item logging — three files exceed
the ceiling: finbert source (8 KB), koala-machine-state (7.1 KB),
litellm-absorption (8.8 KB). Curated knowledge entries should never be
vector-blind.
Approach: chunk-before-embed, no schema change.
vectorstore/chunk.go (new)
- ChunkMarkdown splits at H1/H2 boundaries; sections over maxBytes are
further split at paragraph boundaries, packing greedily under budget.
- NumberChunks assigns "<parent>#NNNN" storage paths (1-based, zero-padded
to 4 digits — handles files with up to ~10k sections in stable sort order).
- ParentPath strips the chunk suffix for retrieval-side dedup.
vectorstore/sync.go
- After ChunkMarkdown produces N pieces, each is embedded + upserted as a
separate brain_embeddings row at "<parent>#NNNN". maxChunkBytes = 4000
(≈1000 nomic tokens, well under the 2048 ceiling with headroom for
unicode/code blocks).
- "Already embedded?" check now reduces known paths to parent set via
ParentPath, so the first chunk hit short-circuits the file.
- Delete walk also reduces via ParentPath; when a parent file disappears,
every chunk row (and any pre-existing bare-path row, for backward
compatibility with rows written before this change) gets dropped.
search/search.go
- hybridMerge collapses chunk-path vector hits to parent via ParentPath
before scope check, RRF accumulation, and hydration. A file with three
chunk hits returns one result row, not three.
Backward compatibility: pre-existing bare-path rows in brain_embeddings
keep working — ParentPath returns them unchanged, knownParents handles
them as if they were "wiki/foo.md#NNNN" hits, sync skips re-embed, and
search dedup is a no-op for them. No migration required to ship.
Tests:
- chunk_test.go covers short / heading split / oversized section /
content preservation / chunk numbering / parent-path stripping.
- sync_test.go adds long-file chunking, single-chunk-row short file,
skip-if-any-chunk-known, delete-all-chunks-of-disappeared-file.
Existing tests updated for #NNNN paths.
- search_test.go adds chunk-paths-dedupe-to-parent.
Closes gitea/mathias/infra#38.
The embed sync goroutine only walked brain/wiki/. brain/knowledge/ (112
curated entries, per CLAUDE.md the most-important brain content) had zero
coverage in brain_embeddings — vector retrieval was blind to it. Hybrid
BM25 + pgvector retrieval would never surface a curated knowledge entry
via the vector arm.
Extract the per-root walk into a loop over a small subdir list and add
"knowledge" alongside "wiki". scanDirs is package-level so it stays a
single source of truth for what gets embedded.
Also log each failing item's path + error string from StartSync.
Previously only the aggregate count was logged, so a persistent
`errors=1` per cycle was opaque. With per-item warnings, the actual
ollama "input length exceeds the context length" surface immediately.
Refs gitea/mathias/infra#37 (this commit covers the knowledge/ scan
bug; the long-file chunking bug is a separate change.)
Wires nomic-embed-text (iguana ollama) + pgvector on the shared
postgres18 into brain_query / brain_answer via Reciprocal Rank Fusion.
Pure BM25 stays the default; setting BRAIN_PG_DSN and BRAIN_EMBED_URL
together opts in. Setting one without the other is misconfiguration →
exit 1.
New packages:
- internal/embed
Client.Embed(ctx, text) → []float32 via POST {URL}/api/embed.
Defaults to nomic-embed-text:latest (768 dim). nil-on-empty-URL so
callers gate on a single nil check.
- internal/vectorstore
PGStore wraps a pgxpool against postgres18. Init creates
brain_embeddings(path PK, vector(768), updated_at) + HNSW cosine
index idempotently. Upsert / Delete / Search / KnownPaths.
Sync(brainDir, store, embedder) diffs brain/wiki/ against the store
and upserts new files / deletes removed ones; StartSync runs it on
a ticker (default 300s). Integration tests gated by BRAIN_PG_TEST_DSN.
- scripts/brain-embeddings-init.sql
One-time DBA setup: brain DB, brain_app role, vector extension,
GRANTs. Idempotent.
Search layer:
- search.QueryOptions gains Vector + Embedder fields.
- QueryContext is the cancellable variant; Query stays for callers.
- When both are set, BM25 (top-N) and pgvector (top-4N) candidates
merge via Reciprocal Rank Fusion (k=60, Cormack et al. 2009 — no
tuning knob, robust to scale differences between rankers).
- Vector-only hits are hydrated from disk so callers see uniform
Result records (path, title, excerpt, wing, hall, score).
- Wing/hall filters still apply to vector candidates via path-prefix.
- On embedder/vector errors the search falls back to BM25 — embedding
outage degrades quality but doesn't take the brain offline.
MCP wiring:
- mcp.Server.WithHybridRetrieval(v, e) opt-in setter, same shape as
WithReranker.
- brainQuery and brainAnswer pass the wired vector/embedder through
to search.QueryContext.
REST:
- POST /backfill-embeddings drives Sync synchronously. Returns
{added, deleted, errors[]}. 503 when feature is unconfigured.
cmd/server/main.go:
- BRAIN_PG_DSN + BRAIN_EMBED_URL together enable hybrid; one alone
→ exit 1.
- vectorAdapter bridges *PGStore (returns []Hit) to
search.VectorSearcher (which takes []VectorHit) without either
package importing the other.
- BRAIN_EMBED_SYNC_INTERVAL (default 300s) controls the background
Sync ticker.
Backend pivot from Qdrant to pgvector recorded in DECISIONS.md
2026-05-18 (supersedes 2026-04-08): postgres18 already runs in
databases/ ns, Qdrant was never deployed, one engine beats two.
Dependency: github.com/jackc/pgx/v5 — modern, native pgvector via
parametric vector literals.
Tests:
- embed.Client: empty-URL nil, request shape, dimension, upstream
error propagation, empty-text rejection.
- vectorstore.PGStore: dimension validation (unit); upsert/search/
KnownPaths (integration, BRAIN_PG_TEST_DSN-gated).
- vectorstore.Sync: adds new files, skips known, deletes
disappeared, skips _index.md, no-op when nil, collects embedder
errors.
- search.Query: hybrid promotes vector-only hits via RRF; falls
back to BM25 on embedder error.
Closes hyperguild#8.
mathiasandClaude Opus 5.5