fix(ingestion): embed sync also scans brain/knowledge/ + logs per-item errors

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.)

ingestion/internal/vectorstore/sync.go

@@ -32,7 +32,13 @@ type SyncResult struct {
 	Errors  []error
 }
 
-// Sync brings the embedding store in line with brain/wiki/ on disk:
+// scanDirs is the set of brainDir subdirectories whose .md files are
+// embedded for vector retrieval. wiki/ holds LLM-extracted entity and
+// source pages; knowledge/ holds curated hand-written entries.
+var scanDirs = []string{"wiki", "knowledge"}
+
+// Sync brings the embedding store in line with brain/{wiki,knowledge}/
+// on disk:
 //   - new files (in the tree, not in the store) get embedded + upserted
 //   - files whose mtime exceeds the store's updated_at get re-embedded
 //   - files no longer on disk get deleted from the store
@@ -51,50 +57,52 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 	}
 	seen := make(map[string]struct{})
 
-	wikiDir := filepath.Join(brainDir, "wiki")
+	for _, sub := range scanDirs {
-	if _, err := os.Stat(wikiDir); os.IsNotExist(err) {
+		root := filepath.Join(brainDir, sub)
-		return res, nil
+		if _, err := os.Stat(root); os.IsNotExist(err) {
-	}
+			continue
+		}
 
-	err = filepath.WalkDir(wikiDir, func(path string, d os.DirEntry, err error) error {
+		err = filepath.WalkDir(root, func(path string, d os.DirEntry, err error) error {
+			if err != nil {
+				return err
+			}
+			if d.IsDir() || !strings.HasSuffix(path, ".md") || d.Name() == "_index.md" {
+				return nil
+			}
+			rel, err := filepath.Rel(brainDir, path)
+			if err != nil {
+				return err
+			}
+			relSlash := filepath.ToSlash(rel)
+			seen[relSlash] = struct{}{}
+
+			if _, ok := known[relSlash]; ok {
+				// Already embedded — TODO: compare mtime once Store exposes
+				// updated_at so we re-embed on edit. For now, skip.
+				return nil
+			}
+
+			content, readErr := os.ReadFile(path)
+			if readErr != nil {
+				res.Errors = append(res.Errors, fmt.Errorf("read %s: %w", relSlash, readErr))
+				return nil
+			}
+			vec, embErr := embedder.Embed(ctx, string(content))
+			if embErr != nil {
+				res.Errors = append(res.Errors, fmt.Errorf("embed %s: %w", relSlash, embErr))
+				return nil
+			}
+			if upErr := store.Upsert(ctx, relSlash, vec); upErr != nil {
+				res.Errors = append(res.Errors, fmt.Errorf("upsert %s: %w", relSlash, upErr))
+				return nil
+			}
+			res.Added++
+			return nil
+		})
 		if err != nil {
-			return err
+			return res, fmt.Errorf("walk %s: %w", sub, err)
 		}
-		if d.IsDir() || !strings.HasSuffix(path, ".md") || d.Name() == "_index.md" {
-			return nil
-		}
-		rel, err := filepath.Rel(brainDir, path)
-		if err != nil {
-			return err
-		}
-		relSlash := filepath.ToSlash(rel)
-		seen[relSlash] = struct{}{}
-
-		if _, ok := known[relSlash]; ok {
-			// Already embedded — TODO: compare mtime once Store exposes
-			// updated_at so we re-embed on edit. For now, skip.
-			return nil
-		}
-
-		content, readErr := os.ReadFile(path)
-		if readErr != nil {
-			res.Errors = append(res.Errors, fmt.Errorf("read %s: %w", relSlash, readErr))
-			return nil
-		}
-		vec, embErr := embedder.Embed(ctx, string(content))
-		if embErr != nil {
-			res.Errors = append(res.Errors, fmt.Errorf("embed %s: %w", relSlash, embErr))
-			return nil
-		}
-		if upErr := store.Upsert(ctx, relSlash, vec); upErr != nil {
-			res.Errors = append(res.Errors, fmt.Errorf("upsert %s: %w", relSlash, upErr))
-			return nil
-		}
-		res.Added++
-		return nil
-	})
-	if err != nil {
-		return res, fmt.Errorf("walk wiki: %w", err)
 	}
 
 	// Drop rows whose file is gone.
@@ -125,6 +133,9 @@ func StartSync(ctx context.Context, brainDir string, store Store, embedder Embed
 			slog.Error("embed sync failed", "err", err)
 		} else if r.Added+r.Deleted > 0 || len(r.Errors) > 0 {
 			slog.Info("embed sync", "added", r.Added, "deleted", r.Deleted, "errors", len(r.Errors))
+			for _, e := range r.Errors {
+				slog.Warn("embed sync item failed", "err", e)
+			}
 		}
 		for {
 			select {

ingestion/internal/vectorstore/sync_test.go

@@ -117,6 +117,20 @@ func TestSync_SkipsIndexFiles(t *testing.T) {
 	assert.NotContains(t, store.upserts, "wiki/a/_index.md")
 }
 
+func TestSync_ScansKnowledgeDir(t *testing.T) {
+	dir := t.TempDir()
+	writeNote(t, dir, "wiki/a/facts/x.md", "x")
+	writeNote(t, dir, "knowledge/2026-05-19-koala-gpu-setup.md", "knowledge body")
+
+	store := &stubStore{known: map[string]struct{}{}}
+	emb := stubEmbedder{vec: make([]float32, 768)}
+	res, err := vectorstore.Sync(context.Background(), dir, store, emb)
+	require.NoError(t, err)
+	assert.Equal(t, 2, res.Added)
+	assert.Contains(t, store.upserts, "wiki/a/facts/x.md")
+	assert.Contains(t, store.upserts, "knowledge/2026-05-19-koala-gpu-setup.md")
+}
+
 func TestSync_NoOpWhenComponentsNil(t *testing.T) {
 	dir := t.TempDir()
 	writeNote(t, dir, "wiki/a/facts/x.md", "x")