daftari 1.30.0 → 1.32.0

package/dist/okf/types.js

@@ -0,0 +1,82 @@
+// Open Knowledge Format (OKF) — shared constants and types.
+//
+// OKF is Google Cloud's vendor-neutral specification (v0.2) for the LLM-wiki
+// pattern: a directory of markdown files with YAML frontmatter that any
+// producer can emit and any consumer can read without translation. Daftari's
+// vault *is* this pattern, so `daftari okf export|import` bridges the two.
+//
+// Spec essentials that this module implements:
+//   - A concept doc is any non-reserved `.md` file with a frontmatter block.
+//   - The single required frontmatter field is `type` (a free-form kind string).
+//   - Recommended fields: title, description, resource, tags.
+//   - Reserved filenames: index.md (progressive-disclosure listing) and log.md
+//     (chronological change history, newest first).
+//   - Consumers must tolerate unknown fields and unknown `type` values.
+//
+// v0.2 adds opt-in trust signals — raw credibility indicators, never computed
+// scores, all optional so v0.1 bundles stay valid:
+//   - `generated: {by, at}` — who produced the content and when it last
+//     meaningfully changed. Renames v0.1 `timestamp` (consumers fall back).
+//   - `verified: [{by, at}]` — independent confirmations. The trust tier is
+//     derived: no key = unverified, machine actors only = machine-confirmed,
+//     any `human:<id>` entry = human-reviewed.
+//   - `status: draft | stable | deprecated` — lifecycle; absent means stable.
+//   - `stale_after: YYYY-MM-DD` — absolute date (not a TTL) for deterministic
+//     staleness checks.
+//   - `sources: [{id, resource, title, author, usage_count, last_modified}]`
+//     — structured provenance. Renames the v0.1 body `# Citations` list.
+//   - A new concept type, `Attested Computation`: a sanctioned computation
+//     agents may parameterize but never edit.
+// The OKF spec version this producer targets and this consumer understands.
+// Written into the exported bundle's root index.md frontmatter (the spec's
+// place for a bundle to declare its target version).
+export const OKF_VERSION = "0.2";
+// Reserved filenames with defined structural meaning. They are NOT concept
+// docs: export generates them, import skips them.
+export const OKF_INDEX_FILE = "index.md";
+export const OKF_LOG_FILE = "log.md";
+export const OKF_RESERVED_FILES = [OKF_INDEX_FILE, OKF_LOG_FILE];
+// The frontmatter key under which export stashes the document's original,
+// verbatim Daftari frontmatter. It is an ordinary producer-defined field as far
+// as OKF is concerned (consumers preserve it), but it lets `okf import` of a
+// Daftari-produced bundle reconstruct the source frontmatter exactly rather than
+// re-synthesizing it from the lossy OKF core fields. Absent on foreign bundles.
+export const DAFTARI_SIDECAR_KEY = "daftari";
+// The `type` value assigned to a concept doc that has no natural kind to map
+// from (an untitled/uncollected doc on export, a foreign doc with no directory
+// on import). OKF requires a non-empty `type`; this keeps every emitted doc
+// conformant without inventing a false-specific kind.
+export const DEFAULT_OKF_TYPE = "note";
+// The Daftari collection assigned to a foreign OKF concept doc that carries no
+// directory and no usable `type` to derive one from.
+export const DEFAULT_IMPORT_COLLECTION = "imported";
+// The canonical OKF frontmatter fields, in the order export writes them. `type`
+// is the only required one; the rest are recommended/optional and omitted when
+// empty. `timestamp` is the v0.1 name for `generated.at` — export writes the
+// v0.2 form, import still accepts the old one.
+export const OKF_CORE_FIELDS = [
+    "type",
+    "title",
+    "description",
+    "resource",
+    "tags",
+    "generated",
+    "verified",
+    "status",
+    "stale_after",
+    "sources",
+];
+// The v0.2 lifecycle states. Absence means "stable" per spec.
+export const OKF_STATUSES = ["draft", "stable", "deprecated"];
+// The v0.2 concept type for a sanctioned computation. Agents may fill declared
+// parameters at call time but must never edit the computation itself. Import
+// flags these docs in a warning so an operator can grant `tier: source` via
+// vault_set_tier — it never auto-elevates, because a foreign bundle's
+// self-declared type is not an authorization for write-protection enforcement.
+export const OKF_ATTESTED_COMPUTATION_TYPE = "Attested Computation";
+// Prefix under which import preserves foreign OKF fields that have no lossless
+// Daftari mapping (the trust record, attestation machinery, and any unknown
+// producer-defined fields). Keeps the import non-destructive, mirroring what
+// the `daftari` sidecar does in the export direction.
+export const OKF_PRESERVED_PREFIX = "okf_";
+//# sourceMappingURL=types.js.map

package/dist/okf/types.js.map

@@ -0,0 +1 @@
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package/dist/search/coverage.d.ts.map

@@ -1 +1 @@
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package/dist/search/coverage.js

@@ -59,7 +59,7 @@ export function computeWindow(db, hits, entity, opts) {
     const dates = [];
     for (const h of hits.slice(0, opts.seedK)) {
         const d = getDocument(db, h.path);
-        if (d && d.tags.includes(entity) && d.created && isValidIsoDate(d.created))
+        if (d?.tags.includes(entity) && d.created && isValidIsoDate(d.created))
             dates.push(d.created);
     }
     if (dates.length === 0)

package/dist/search/coverage.js.map

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package/dist/search/hybrid.d.ts

@@ -21,15 +21,34 @@ export interface HybridHit {
     currentSource?: CurrentSource;
     contested?: ContestedTension[];
     contestedCount?: number;
+    pendingBrokenUpstream?: "some" | "many";
+    hiddenPendingUpstream?: "some" | "many";
+    orphan?: boolean;
+    deprecatedStillLinked?: boolean;
     viaCoverage?: boolean;
     coverageReason?: "edge" | "entity-window";
 }
+export interface RerankCandidate {
+    rank: number;
+    path: string;
+    title: string;
+    collection: string;
+    status: string;
+    score: number;
+    bm25Score: number;
+    vectorScore: number;
+    snippet: string;
+}
 export interface HybridSearchResult {
     query: string;
     count: number;
     vectorUsed: boolean;
     weights: HybridWeights;
     hits: HybridHit[];
+    rerank?: {
+        instructions: string;
+        candidates: RerankCandidate[];
+    };
 }
 export interface HybridSearchOptions {
     weights?: HybridWeights;

package/dist/search/hybrid.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hybrid.d.ts","sourceRoot":"","sources":["../../src/search/hybrid.ts"],"names":[],"mappings":"AAkBA,OAAO,EAAgB,KAAK,UAAU,EAAE,MAAM,sBAAsB,CAAC;AACrE,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAKL,KAAK,OAAO,EACb,MAAM,wBAAwB,CAAC;AAEhC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AACvD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AAGzD,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,eAAO,MAAM,eAAe,EAAE,aAA0C,CAAC;AAEzE,MAAM,WAAW,SAAS;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,UAAU,GAAG,IAAI,CAAC;IACzB,aAAa,CAAC,EAAE,aAAa,CAAC;IAC9B,SAAS,CAAC,EAAE,gBAAgB,EAAE,CAAC;IAC/B,cAAc,CAAC,EAAE,MAAM,CAAC;IAOxB,qBAAqB,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAGxC,qBAAqB,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAKxC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,qBAAqB,CAAC,EAAE,OAAO,CAAC;IAChC,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,cAAc,CAAC,EAAE,MAAM,GAAG,eAAe,CAAC;CAC3C;AAOD,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;IACnB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,kBAAkB;IACjC,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,OAAO,CAAC;IACpB,OAAO,EAAE,aAAa,CAAC;IACvB,IAAI,EAAE,SAAS,EAAE,CAAC;IAKlB,MAAM,CAAC,EAAE;QAAE,YAAY,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,eAAe,EAAE,CAAA;KAAE,CAAC;CAClE;AAiUD,MAAM,WAAW,mBAAmB;IAClC,OAAO,CAAC,EAAE,aAAa,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,kBAAkB,CAAC,EAAE,UAAU,GAAG,OAAO,CAAC;IAQ1C,SAAS,CAAC,EAAE,OAAO,CAAC;CACrB;AAGD,wBAAsB,YAAY,CAChC,EAAE,EAAE,OAAO,EACX,KAAK,EAAE,MAAM,EACb,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,MAAM,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAqC5C;AAED,MAAM,WAAW,mBAAmB;IAClC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,OAAO,CAAC;IACpB,OAAO,EAAE,aAAa,CAAC;IACvB,IAAI,EAAE,SAAS,EAAE,CAAC;CACnB;AAOD,wBAAgB,aAAa,CAC3B,EAAE,EAAE,OAAO,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,mBAAwB,GAChC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CA4CpC"}

package/dist/search/hybrid.js

@@ -16,7 +16,7 @@
 // unavailable) or the index holds no embeddings, the search degrades to
 // lexical-only and reports vectorUsed: false rather than failing.
 import { computeDecay } from "../curation/decay.js";
-import { ok } from "../frontmatter/types.js";
+import { err, ok } from "../frontmatter/types.js";
 import { embeddingToBlob, getChunksForPath, getDocument, getDocumentsByPaths, } from "../storage/index-db.js";
 import { buildMatchQuery, tokenize } from "./bm25.js";
 import { embedQuery, getProvider, meanEmbedding } from "./vector.js";
@@ -151,23 +151,43 @@ function vecRanking(db, queryEmbedding, modelId) {
     }
     return result;
 }
+// snippet() excerpt budget, in tokens. ~48 stemmed tokens lands near the
+// ~280 chars the JS fallback (SNIPPET_RADIUS * 2) produces, so lexical and
+// fallback snippets read at comparable length.
+const FTS_SNIPPET_TOKENS = 48;
 // Chunk-level lexical ranking. Runs an FTS5 MATCH over `chunks_fts` (one row
 // per chunk), reads the inverse bm25 (flip to larger=better), joins back to
 // `chunks` on rowid to map onto document paths, and collapses to each
 // document's BEST chunk score (max) — mirroring vecRanking's best-per-doc.
 // A relevant topic's own chunk scores high even when its whole document is
-// long and multi-topic. Null query (no usable tokens) returns an empty map.
+// long and multi-topic. Null query (no usable tokens) returns empty maps.
+//
+// The same pass captures each document's excerpt via FTS5 snippet() from its
+// best-scoring chunk (#108): the inverted index centres the excerpt on the
+// actual match — stemmed variants included, which the JS fallback's literal
+// indexOf cannot see — and no full body is scanned in JS. snippet() is
+// legal here because chunks_fts is EXTERNAL-CONTENT (content='chunks') with
+// a matching column name; documents_fts declares content_body over a base
+// column named content, so the document-granularity path deliberately keeps
+// the JS fallback instead of a schema migration.
 function chunkFtsRanking(db, query) {
     if (query === null)
-        return new Map();
+        return { scores: new Map(), snippets: new Map() };
     const rows = db
-        .prepare(`SELECT c.path AS path, -bm25(chunks_fts) AS score
+        .prepare(`SELECT c.path AS path, chunks_fts.rowid AS crowid, -bm25(chunks_fts) AS score
          FROM chunks_fts
          JOIN chunks AS c ON c.rowid = chunks_fts.rowid
         WHERE chunks_fts MATCH ?
         ORDER BY bm25(chunks_fts)`)
         .all(query);
-    const result = new Map();
+    const scores = new Map();
+    // The winning chunk's FTS rowid per path — the snippet pass below is
+    // restricted to exactly these rows, so snippet()'s tokenize/format cost is
+    // paid once per DOCUMENT, not once per matched chunk. (A ROW_NUMBER()
+    // window subquery would not help here: the projected snippet() is still
+    // evaluated per inner row before the window filter, and FTS5 auxiliary
+    // functions cannot move outside the MATCH cursor.)
+    const winners = new Map();
     for (const r of rows) {
         // Some rows may produce a non-positive flipped score if FTS5 returned a
         // positive bm25 (rare with prefix matches); drop them so the normalize
@@ -179,11 +199,31 @@ function chunkFtsRanking(db, query) {
         // their raw scores are never directly compared.
         if (r.score <= 0)
             continue;
-        const prev = result.get(r.path) ?? -Infinity;
-        if (r.score > prev)
-            result.set(r.path, r.score);
+        const prev = scores.get(r.path) ?? -Infinity;
+        if (r.score > prev) {
+            scores.set(r.path, r.score);
+            // Keying on the max KEPT score guarantees the snippet always comes
+            // from the same chunk the document's score does.
+            winners.set(r.path, r.crowid);
+        }
     }
-    return result;
+    const snippets = new Map();
+    if (winners.size > 0) {
+        const ids = [...winners.values()];
+        const placeholders = ids.map(() => "?").join(",");
+        const snips = db
+            .prepare(`SELECT c.path AS path, snippet(chunks_fts, 0, '', '', '…', ?) AS snip
+           FROM chunks_fts
+           JOIN chunks AS c ON c.rowid = chunks_fts.rowid
+          WHERE chunks_fts MATCH ? AND chunks_fts.rowid IN (${placeholders})`)
+            .all(FTS_SNIPPET_TOKENS, query, ...ids);
+        for (const s of snips) {
+            const collapsed = s.snip.replace(/\s+/g, " ").trim();
+            if (collapsed.length > 0)
+                snippets.set(s.path, collapsed);
+        }
+    }
+    return { scores, snippets };
 }
 // Core ranker shared by query search and related-document search.
 // `matchQuery` is the FTS5 MATCH string (already prefix-OR'd, or null);
@@ -193,13 +233,18 @@ function chunkFtsRanking(db, query) {
 // matching term — it doesn't drive ranking.
 function rankDocuments(db, matchQuery, queryEmbedding, queryTokensForSnippet, opts) {
     let bm25Norm;
+    // Best-chunk excerpts from the lexical pass (#108); empty for the
+    // document-granularity path, whose hits fall back to the JS scan.
+    let lexicalSnippets = new Map();
     if (opts.lexicalGranularity === "chunk") {
         // Body granularity (the dilution fix) TIERED with a clean title/tag signal
         // (the native-shape fix). Each is normalized to its own max to reconcile the
         // two FTS score scales; tieredLexical then ranks every body match above every
         // title-only match. The title/tag signal reuses ftsRanking with a column-
         // restricted query so it scores title+tags only (no body dilution).
-        const chunkNorm = normalize(chunkFtsRanking(db, matchQuery));
+        const chunkRanked = chunkFtsRanking(db, matchQuery);
+        lexicalSnippets = chunkRanked.snippets;
+        const chunkNorm = normalize(chunkRanked.scores);
         const titleTagNorm = normalize(ftsRanking(db, columnRestrict(matchQuery, "{title tags}")));
         bm25Norm = tieredLexical(chunkNorm, titleTagNorm);
     }
@@ -246,7 +291,10 @@ function rankDocuments(db, matchQuery, queryEmbedding, queryTokensForSnippet, op
             score,
             bm25Score,
             vectorScore,
-            snippet: makeSnippet(doc.content, queryTokensForSnippet),
+            // FTS5's excerpt for lexical hits (#108); the JS body scan remains the
+            // fallback for vector-only and title/tag-only hits, which have no
+            // matched body chunk to centre on.
+            snippet: lexicalSnippets.get(path) ?? makeSnippet(doc.content, queryTokensForSnippet),
             decay: computeDecay({
                 status: doc.status,
                 confidence: doc.confidence,
@@ -309,10 +357,7 @@ export function relatedSearch(db, path, options = {}) {
     const rankLimit = options.overFetch ? Number.POSITIVE_INFINITY : limit;
     const doc = getDocument(db, path);
     if (!doc) {
-        return {
-            ok: false,
-            error: new Error(`document not indexed: ${path} (try vault_reindex)`),
-        };
+        return err(new Error(`document not indexed: ${path} (try vault_reindex)`));
     }
     const provider = getProvider();
     const chunkVectors = getChunksForPath(db, path, provider.id, provider.dim)

package/dist/search/hybrid.js.map

@@ -1 +1 @@
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package/dist/search/reindex.d.ts

@@ -1,4 +1,7 @@
 import { type Result } from "../frontmatter/types.js";
+import { type IndexDb } from "../storage/index-db.js";
+export declare function readManifest(db: IndexDb): Record<string, number> | null;
+export declare function writeManifest(db: IndexDb, manifest: Record<string, number>): void;
 export declare function isIndexFresh(vaultRoot: string): Promise<boolean>;
 export interface FlaggedDocument {
     path: string;
@@ -17,6 +20,7 @@ export interface ReindexResult {
 }
 export interface ReindexOptions {
     onProgress?: (done: number, total: number) => void;
+    embedCommitBatch?: number;
 }
 export declare function reindexWarnings(result: ReindexResult): string[];
 export declare function reindexVault(vaultRoot: string, opts?: ReindexOptions): Promise<Result<ReindexResult, Error>>;

package/dist/search/reindex.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reindex.d.ts","sourceRoot":"","sources":["../../src/search/reindex.ts"],"names":[],"mappings":"AAuBA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAmH/D,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CActE;AAMD,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IAGvB,OAAO,EAAE,eAAe,EAAE,CAAC;IAM3B,kBAAkB,EAAE,eAAe,EAAE,CAAC;IACtC,SAAS,EAAE,MAAM,CAAC;IAIlB,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED,MAAM,WAAW,cAAc;IAM7B,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,CAAC;CACpD;AAOD,wBAAgB,eAAe,CAAC,MAAM,EAAE,aAAa,GAAG,MAAM,EAAE,CAc/D;AA0ID,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,KAAK,CAAC,CAAC,CAyHvC;AAED,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IAKvB,kBAAkB,EAAE,MAAM,GAAG,IAAI,CAAC;CACnC;AASD,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CAmH7C"}
+{"version":3,"file":"reindex.d.ts","sourceRoot":"","sources":["../../src/search/reindex.ts"],"names":[],"mappings":"AAwBA,OAAO,EAAW,KAAK,MAAM,EAAE,MAAM,yBAAyB,CAAC;AAC/D,OAAO,EAUL,KAAK,OAAO,EASb,MAAM,wBAAwB,CAAC;AAmEhC,wBAAgB,YAAY,CAAC,EAAE,EAAE,OAAO,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAUvE;AAED,wBAAgB,aAAa,CAAC,EAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAEjF;AAgBD,wBAAsB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CActE;AAMD,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IAGvB,OAAO,EAAE,eAAe,EAAE,CAAC;IAM3B,kBAAkB,EAAE,eAAe,EAAE,CAAC;IACtC,SAAS,EAAE,MAAM,CAAC;IAIlB,aAAa,EAAE,MAAM,CAAC;IACtB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED,MAAM,WAAW,cAAc;IAM7B,UAAU,CAAC,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,KAAK,IAAI,CAAC;IAInD,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAeD,wBAAgB,eAAe,CAAC,MAAM,EAAE,aAAa,GAAG,MAAM,EAAE,CAc/D;AA8ID,wBAAsB,YAAY,CAChC,SAAS,EAAE,MAAM,EACjB,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,MAAM,CAAC,aAAa,EAAE,KAAK,CAAC,CAAC,CA0IvC;AAED,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,OAAO,CAAC;IAKvB,kBAAkB,EAAE,MAAM,GAAG,IAAI,CAAC;CACnC;AASD,wBAAsB,aAAa,CACjC,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,mBAAmB,EAAE,KAAK,CAAC,CAAC,CA+I7C"}

package/dist/search/reindex.js

@@ -19,9 +19,10 @@
 import { stat } from "node:fs/promises";
 import { rebuildEdgesIndex } from "../curation/edges.js";
 import { rebuildStagedActionsIndex } from "../curation/staged-actions.js";
+import { buildPathIndexes, extractLinks, outgoingLinkTargets } from "../curation/vault-docs.js";
 import { parseDocument } from "../frontmatter/parser.js";
 import { err, ok } from "../frontmatter/types.js";
-import { clearEmbeddingsVec, clearIndex, deleteDocument, documentCount, existingEmbeddingHashes, gcOrphanedEmbeddings, getMeta, insertChunkRow, insertDocument, insertEmbedding, insertEmbeddingVec, openIndexDb, setMeta, } from "../storage/index-db.js";
+import { allDocumentPaths, clearEmbeddingsVec, clearIndex, deleteDocument, documentCount, existingEmbeddingHashes, gcOrphanedEmbeddings, getMeta, insertChunkRow, insertDocument, insertEmbedding, insertEmbeddingVec, openIndexDb, replaceDocLinks, setMeta, } from "../storage/index-db.js";
 import { listFiles, readFile, resolveVaultPath } from "../storage/local.js";
 import { sha256Hex } from "../utils/hash.js";
 import { tokenize } from "./bm25.js";
@@ -82,7 +83,7 @@ async function buildManifest(vaultRoot) {
     }
     return manifest;
 }
-function readManifest(db) {
+export function readManifest(db) {
     const raw = getMeta(db, MANIFEST_META_KEY);
     if (!raw)
         return null;
@@ -96,7 +97,7 @@ function readManifest(db) {
         return null;
     }
 }
-function writeManifest(db, manifest) {
+export function writeManifest(db, manifest) {
     setMeta(db, MANIFEST_META_KEY, JSON.stringify(manifest));
 }
 function manifestsMatch(a, b) {
@@ -134,6 +135,13 @@ export async function isIndexFresh(vaultRoot) {
         db.close();
     }
 }
+// #54: embeddings land in the durable content-addressed cache PER BATCH, not
+// in one end-of-build transaction. The cache thereby doubles as the resume
+// checkpoint: a process-lock takeover SIGTERM mid-build loses at most one
+// batch, and the next build's existingEmbeddingHashes() pass sees every
+// committed batch as a cache hit and embeds only the remainder — no cursor,
+// no new state, the table the build already consults IS the watermark.
+const EMBED_COMMIT_BATCH = 64;
 // Human-readable warning lines for a reindex result's `skipped` and
 // `invalidFrontmatter` buckets, or [] when both are empty. Callers write these
 // to stderr so documents missing from the index — or indexed with coerced
@@ -241,10 +249,14 @@ async function stageDocuments(vaultRoot) {
 // which model produced the vectors.
 function writeChunkRows(db, staged) {
     let chunkCount = 0;
+    // Link resolution runs against the FULL staged path set, built up front —
+    // insertion order can never drop an edge whose target lands later (#8).
+    const linkIndexes = buildPathIndexes(staged.map(({ doc }) => ({ path: doc.path })));
     const write = db.transaction(() => {
         clearIndex(db);
         for (const { doc, chunks, hashes } of staged) {
             insertDocument(db, doc);
+            replaceDocLinks(db, doc.path, outgoingLinkTargets(doc.content, doc.path, linkIndexes));
             chunks.forEach((text, chunkIndex) => {
                 const row = {
                     path: doc.path,
@@ -304,14 +316,31 @@ export async function reindexVault(vaultRoot, opts = {}) {
         const missHashes = [...missTextByHash.keys()];
         const missTexts = missHashes.map((h) => missTextByHash.get(h) ?? "");
         const totalChunks = allHashes.length;
-        const cacheHits = totalChunks - allHashes.filter((h) => !cached.has(h)).length;
+        let cacheHits = 0;
+        for (const h of allHashes)
+            if (cached.has(h))
+                cacheHits += 1;
         let vectorEnabled = true;
+        let committedEmbeds = 0;
         if (missTexts.length > 0) {
-            const embedResult = await embed(missTexts, opts.onProgress);
-            if (embedResult.ok) {
+            const batchSize = opts.embedCommitBatch ?? EMBED_COMMIT_BATCH;
+            for (let start = 0; start < missHashes.length; start += batchSize) {
+                const sliceHashes = missHashes.slice(start, start + batchSize);
+                const sliceTexts = missTexts.slice(start, start + batchSize);
+                const embedResult = await embed(sliceTexts, opts.onProgress
+                    ? (done, _total) => opts.onProgress?.(committedEmbeds + done, missHashes.length)
+                    : undefined);
+                if (!embedResult.ok) {
+                    // Model unavailable (or died mid-build). Batches already committed
+                    // stay in the cache — the next build resumes past them. Documents
+                    // + chunk rows still land below so BM25 works; vector ranking
+                    // degrades to nothing for this reindex.
+                    vectorEnabled = false;
+                    break;
+                }
                 const writeEmbeds = db.transaction(() => {
-                    for (let i = 0; i < missHashes.length; i++) {
-                        const h = missHashes[i] ?? "";
+                    for (let i = 0; i < sliceHashes.length; i++) {
+                        const h = sliceHashes[i] ?? "";
                         const vec = embedResult.value[i];
                         if (!vec)
                             continue;
@@ -319,11 +348,7 @@ export async function reindexVault(vaultRoot, opts = {}) {
                     }
                 });
                 writeEmbeds();
-            }
-            else {
-                // Model unavailable. We still want documents + chunk rows so BM25
-                // works; vector ranking simply degrades to nothing for this reindex.
-                vectorEnabled = false;
+                committedEmbeds += sliceHashes.length;
             }
         }
         else if (totalChunks === 0) {
@@ -369,7 +394,9 @@ export async function reindexVault(vaultRoot, opts = {}) {
             skipped,
             invalidFrontmatter,
             indexedAt,
-            embeddedCount: missHashes.length,
+            // COMMITTED count, not attempted: an interrupted build reports what it
+            // actually banked (#54).
+            embeddedCount: committedEmbeds,
             cacheHits,
             orphansRemoved,
         });
@@ -453,9 +480,32 @@ export async function indexDocument(vaultRoot, relPath) {
                 vectorEnabled = false;
             }
         }
+        // Refresh this doc's OUTGOING links against the indexed path universe.
+        // Inbound edges to it update as their sources are re-indexed — a doc
+        // created after a bare-name link to it was indexed stays unlinked until
+        // the linker's next write or a full reindex (accepted
+        // reindex-granularity staleness, #8).
+        //
+        // The path index is O(vault) to build, so it is constructed only when the
+        // document actually links out — and outside the write transaction either
+        // way, to keep the transaction to row writes. The doc's OWN path is added
+        // to the universe (sorted, matching allDocumentPaths' ORDER BY) because a
+        // first-time index runs before this doc's row lands: without it, a bare
+        // link matching the doc's own basename would resolve to a same-basename
+        // sibling instead of being filtered as a self-link.
+        let linkTargets = [];
+        if (extractLinks(doc.content).length > 0) {
+            const universe = allDocumentPaths(db);
+            if (!universe.includes(doc.path)) {
+                universe.push(doc.path);
+                universe.sort();
+            }
+            linkTargets = outgoingLinkTargets(doc.content, doc.path, buildPathIndexes(universe.map((p) => ({ path: p }))));
+        }
         const write = db.transaction(() => {
             deleteDocument(db, doc.path);
             insertDocument(db, doc);
+            replaceDocLinks(db, doc.path, linkTargets);
             chunks.forEach((text, chunkIndex) => {
                 insertChunkRow(db, {
                     path: doc.path,