@monoes/monograph 1.6.1 → 1.6.3

package/dist/src/search/hybrid-query.js

@@ -1,42 +1,102 @@
 /**
- * BM25 search (FTS5) with the historical "hybrid" entry-point signature.
+ * The single lexical retrieval service for the monograph knowledge graph.
  *
- * Monograph search is BM25-only. The former embedding/vector branch
+ * Every adapter — the package-level `monograph_query` MCP tool, the
+ * CLI-hosted `monograph_query` MCP tool, `augmentContext`, the eval server —
+ * calls {@link searchGraph} rather than assembling its own BM25/LIKE/fuzzy
+ * combination. Two adapters answering the same query differently was a real
+ * bug, not a hypothetical one.
+ *
+ * SCORE CONVENTION — higher is better, always non-negative.
+ * SQLite FTS5's `rank` is the opposite (negative, more negative = better).
+ * That inversion is resolved in exactly one place,
+ * {@link relevanceFromFtsRank} in `../storage/fts-store.js`, at the boundary
+ * where a rank enters the system. Nothing downstream ever sees a raw rank, so
+ * the sign cannot be forwarded into a ranker again.
+ *
+ * Monograph search is lexical-only. The former embedding/vector branch
  * (gated on MONOGRAPH_EMBEDDINGS=true) was removed — it was never run in
- * practice (the embeddings table stayed empty) and did a JS cosine full
- * scan. The exported function signatures are unchanged so callers do not
- * need to change.
+ * practice (the embeddings table stayed empty) and did a JS cosine full scan.
+ */
+import { ftsSearch, hybridSearch, relevanceFromFtsRank } from '../storage/fts-store.js';
+/**
+ * Run a lexical search over the graph and return results under the
+ * higher-is-better score convention.
+ *
+ * The query is prepared identically for every mode so that two adapters
+ * asking the same question in the same mode get the same answer.
+ *
+ * Preparation is `trim()` only, deliberately. The FTS5 index uses the trigram
+ * tokenizer, which folds ASCII case but does NOT fold diacritics, and the
+ * index stores `name`/`norm_label` verbatim. Stripping diacritics from the
+ * query (as the old `bm25Query` did) therefore could never *gain* a match —
+ * it only stopped `naïveResolver` from finding the symbol literally named
+ * `naïveResolver`. Lowercasing is likewise skipped: it is a no-op for ASCII
+ * under both the trigram tokenizer and SQLite's LIKE, and for non-ASCII it
+ * would break the LIKE fallback against a capitalized name.
  */
-import { ftsSearch } from '../storage/fts-store.js';
-import { normalizeSearchTerm } from './diacritic.js';
+export function searchGraph(db, query, options = {}) {
+    const { limit = 20, label, mode = 'hybrid' } = options;
+    if (limit <= 0)
+        return [];
+    const normalizedQuery = (query ?? '').trim();
+    if (!normalizedQuery)
+        return [];
+    if (mode === 'bm25') {
+        // Over-fetch a little: FTS5's own ordering is what we keep, but a wider
+        // window gives the caller's label filter something to bite on.
+        const rows = ftsSearch(db, normalizedQuery, Math.max(limit, 50), label);
+        return rows.slice(0, limit).map((r) => ({
+            id: r.id,
+            name: r.name,
+            normLabel: r.normLabel,
+            filePath: r.filePath,
+            label: r.label,
+            relevance: relevanceFromFtsRank(r.rank),
+            startLine: r.startLine,
+            endLine: r.endLine,
+            matchStrategy: 'fts',
+        }));
+    }
+    // hybridSearch already reports a positive, higher-is-better combinedScore
+    // (it routes its FTS rows through relevanceFromFtsRank).
+    return hybridSearch(db, normalizedQuery, limit, label).map((r) => ({
+        id: r.id,
+        name: r.name,
+        normLabel: r.normLabel,
+        filePath: r.filePath,
+        label: r.label,
+        relevance: r.combinedScore,
+        startLine: r.startLine,
+        endLine: r.endLine,
+        matchStrategy: r.matchStrategy,
+    }));
+}
 /**
- * Run a BM25 (FTS5) search. The `embedder` option is ignored — the vector
- * branch was removed; search is BM25-only.
+ * @deprecated Use {@link searchGraph} with `mode: 'bm25'`. Retained as a thin
+ * wrapper so existing callers keep working; it now reports the same
+ * higher-is-better `score` as every other path (it used to forward FTS5's
+ * raw negative `rank`, which inverted ranking for anything downstream that
+ * compared or propagated scores).
  */
 export async function bm25Query(db, query, options = {}) {
     const { limit = 20, label } = options;
-    // Normalize the query for text-based lookups (strip diacritics, lowercase, trim)
-    const normalizedQuery = normalizeSearchTerm(query);
-    // ── BM25 via FTS5 ──────────────────────────────────────────────────────────
-    const bm25Limit = Math.max(limit, 50);
-    const bm25Raw = ftsSearch(db, normalizedQuery, bm25Limit, label);
-    const bm25Results = bm25Raw.map((r) => ({
+    return searchGraph(db, query, { limit, label, mode: 'bm25' }).map((r) => ({
         id: r.id,
         name: r.name,
         normLabel: r.normLabel,
         filePath: r.filePath,
         label: r.label,
-        score: r.rank,
+        score: r.relevance,
         startLine: r.startLine,
         endLine: r.endLine,
     }));
-    return bm25Results.slice(0, limit);
 }
 /**
- * @deprecated Use {@link bm25Query} instead — this is a misleading name
- * (search here is BM25-only, not a hybrid of multiple retrieval strategies).
- * `hybridQuery` remains as an alias for backward compatibility and will be
- * removed in the next major version.
+ * @deprecated Use {@link searchGraph} instead — this is a misleading name
+ * (search here is lexical-only, not a hybrid of multiple retrieval
+ * *modalities*). `hybridQuery` remains as an alias for backward compatibility
+ * and will be removed in the next major version.
  */
 export const hybridQuery = bm25Query;
 //# sourceMappingURL=hybrid-query.js.map

package/dist/src/search/hybrid-query.js.map

@@ -1 +1 @@
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package/dist/src/staleness/git-staleness.d.ts

@@ -1,11 +1,57 @@
 import type { MonographDb } from '../storage/db.js';
+/**
+ * Explicit index freshness. A boolean cannot distinguish "proven up to date"
+ * from "we could not check", and reporting the latter as the former is how a
+ * confident-but-baseless "fresh" answer reaches a caller.
+ *
+ * - `fresh`    — index matches HEAD, worktree is clean, no recorded warnings.
+ * - `stale`    — index is behind HEAD, or the worktree has uncommitted edits.
+ * - `building` — a build lock is held by a live process right now.
+ * - `partial`  — index matches HEAD but is known incomplete (parser warnings
+ *                or a recorded refresh error).
+ * - `unknown`  — freshness could not be determined (git unavailable, no
+ *                recorded revision, or the dirty-worktree probe failed).
+ */
+export type IndexFreshnessState = 'fresh' | 'stale' | 'building' | 'partial' | 'unknown';
 export interface StalenessReport {
+    /**
+     * Commit-divergence only: true when the indexed commit is known to differ
+     * from HEAD (or no commit was recorded). Deliberately unchanged — the
+     * pipeline's skip-when-fresh guard reads it together with `currentCommit`.
+     * It is NOT a freshness verdict: a clean-commit / dirty-worktree index has
+     * `isStale: false` and `state: 'stale'`. New callers should read `state`.
+     */
     isStale: boolean;
+    /** Timestamp of the last build, from `index_meta.indexed_at`. */
     indexedAt: string | null;
+    /** Short (7-char) SHA of the indexed revision. */
     indexedCommit: string | null;
+    /** Short (7-char) SHA of current HEAD. */
     currentCommit: string | null;
     changedSince: string[];
     staleSince: string | null;
+    /** Explicit freshness state — prefer this over `isStale`. */
+    state: IndexFreshnessState;
+    /** One sentence explaining why `state` has this value; safe to show a user. */
+    reason: string;
+    /** Full SHA of the revision the index was built from, null when unrecorded. */
+    indexedRevision: string | null;
+    /** Source scope the index was built with (e.g. 'code-only'), null when unrecorded. */
+    sourceScope: string | null;
+    /** true/false when git could be consulted, null when the probe failed. */
+    dirtyWorktree: boolean | null;
+    /** Sample of uncommitted paths, capped at {@link DIRTY_PATH_CAP}. */
+    dirtyPaths: string[];
+    /** True number of uncommitted paths, null when undetermined. */
+    dirtyFileCount: number | null;
+    /** Parser warnings recorded by the last build, null when none recorded. */
+    parserWarnings: string[] | null;
+    /** Error recorded by the last refresh attempt, null when none recorded. */
+    lastRefreshError: string | null;
+    /** A build lock is currently held by a live process. */
+    buildInProgress: boolean;
+    /** True whenever `state !== 'fresh'`: graph answers may be incomplete. */
+    mayBeIncomplete: boolean;
 }
 export declare function checkStaleness(db: MonographDb, repoPath: string): StalenessReport;
 //# sourceMappingURL=git-staleness.d.ts.map

package/dist/src/staleness/git-staleness.d.ts.map

@@ -1 +1 @@
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package/dist/src/staleness/git-staleness.js

@@ -1,58 +1,216 @@
 import { execSync } from 'node:child_process';
+import { readFileSync } from 'node:fs';
+/** Cap on the dirty-path sample carried in the report; `dirtyFileCount` keeps the true total. */
+const DIRTY_PATH_CAP = 50;
+function readMeta(db) {
+    try {
+        const rows = db.prepare('SELECT key, value FROM index_meta').all();
+        return new Map(rows.map((r) => [r.key, r.value]));
+    }
+    catch {
+        return new Map();
+    }
+}
+/** Accepts either a JSON array or a newline-separated list; null when empty. */
+function parseWarnings(raw) {
+    if (!raw)
+        return null;
+    try {
+        const parsed = JSON.parse(raw);
+        if (Array.isArray(parsed)) {
+            const items = parsed.map(String).filter(Boolean);
+            return items.length > 0 ? items : null;
+        }
+    }
+    catch {
+        /* not JSON — fall through to line parsing */
+    }
+    const lines = raw
+        .split('\n')
+        .map((l) => l.trim())
+        .filter(Boolean);
+    return lines.length > 0 ? lines : null;
+}
+/**
+ * The pipeline serializes builds with a `<dbPath>.build-lock` file holding the
+ * builder's pid. A live holder means a rebuild is under way right now, which is
+ * a different answer than "stale" for a caller deciding whether to wait.
+ */
+function isBuildInProgress(db) {
+    const dbPath = typeof db.name === 'string' ? db.name : '';
+    if (!dbPath || dbPath === ':memory:')
+        return false;
+    let pid;
+    try {
+        pid = Number.parseInt(readFileSync(`${dbPath}.build-lock`, 'utf8'), 10);
+    }
+    catch {
+        return false; // no lock file
+    }
+    if (!Number.isFinite(pid) || pid <= 0)
+        return false;
+    try {
+        process.kill(pid, 0);
+        return true;
+    }
+    catch (err) {
+        // EPERM means the process exists but belongs to another user.
+        return err?.code === 'EPERM';
+    }
+}
+/**
+ * Commit comparison alone cannot see uncommitted work, which is exactly the
+ * code an agent is most likely to ask about. Cheap `git status --porcelain`;
+ * a failure reports "undetermined" rather than "clean".
+ */
+function checkDirtyWorktree(repoPath) {
+    try {
+        const out = execSync('git status --porcelain --no-renames', {
+            cwd: repoPath,
+            encoding: 'utf8',
+            maxBuffer: 8 * 1024 * 1024,
+        });
+        // Porcelain v1 lines are `XY <path>`; ignored files are excluded by default.
+        const paths = out
+            .split('\n')
+            .filter((line) => line.length > 3)
+            .map((line) => line.slice(3).trim())
+            .filter(Boolean);
+        return { dirty: paths.length > 0, paths: paths.slice(0, DIRTY_PATH_CAP), count: paths.length };
+    }
+    catch {
+        return { dirty: null, paths: [], count: null };
+    }
+}
+function buildReport(meta, parts) {
+    return {
+        isStale: parts.isStale,
+        indexedAt: meta.get('indexed_at') ?? null,
+        indexedCommit: parts.indexedCommit,
+        currentCommit: parts.currentCommit,
+        changedSince: parts.changedSince,
+        staleSince: parts.staleSince,
+        state: parts.state,
+        reason: parts.reason,
+        indexedRevision: parts.indexedRevision,
+        sourceScope: meta.get('source_scope') ?? meta.get('scope') ?? null,
+        dirtyWorktree: parts.dirty.dirty,
+        dirtyPaths: parts.dirty.paths,
+        dirtyFileCount: parts.dirty.count,
+        parserWarnings: parseWarnings(meta.get('parser_warnings') ?? meta.get('parse_errors')),
+        lastRefreshError: meta.get('last_refresh_error') ?? null,
+        buildInProgress: parts.state === 'building',
+        mayBeIncomplete: parts.state !== 'fresh',
+    };
+}
+/**
+ * State for an index whose recorded commit equals HEAD. Matching commits are
+ * necessary but not sufficient for "fresh": the worktree may be dirty, the
+ * probe may have failed, or the last build may have recorded problems.
+ */
+function stateForMatchingCommit(meta, dirty) {
+    if (dirty.dirty === null) {
+        return {
+            state: 'unknown',
+            reason: 'Index matches HEAD, but the working tree could not be checked for uncommitted edits.',
+        };
+    }
+    if (dirty.dirty) {
+        return {
+            state: 'stale',
+            reason: `Index matches HEAD but ${dirty.count} path(s) have uncommitted changes that are not in the graph.`,
+        };
+    }
+    const warnings = parseWarnings(meta.get('parser_warnings') ?? meta.get('parse_errors'));
+    const refreshError = meta.get('last_refresh_error') ?? null;
+    if (warnings) {
+        return {
+            state: 'partial',
+            reason: `Index matches HEAD but the last build recorded ${warnings.length} parser warning(s); some symbols may be missing.`,
+        };
+    }
+    if (refreshError) {
+        return {
+            state: 'partial',
+            reason: `Index matches HEAD but the last refresh reported an error: ${refreshError}`,
+        };
+    }
+    return { state: 'fresh', reason: 'Index matches HEAD and the working tree is clean.' };
+}
 export function checkStaleness(db, repoPath) {
-    // 1. Get stored commit hash
-    const row = db.prepare("SELECT value FROM index_meta WHERE key = 'last_commit_hash'").get();
-    const indexedCommitFull = row?.value ?? null;
-    // 2. Get current HEAD (full SHA — --short output length varies by repo size)
+    const meta = readMeta(db);
+    const indexedCommitFull = meta.get('last_commit_hash') ?? null;
+    const indexedCommitShort = indexedCommitFull ? indexedCommitFull.slice(0, 7) : null;
+    const building = isBuildInProgress(db);
+    // 1. Current HEAD (full SHA — `--short` output length varies by repo size)
     let currentCommit = null;
     try {
         currentCommit = execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf8' }).trim();
     }
     catch {
-        // Not a git repo or git not available
-        return {
+        // Not a git repo, no git binary, or a broken checkout. Nothing is known
+        // about freshness here — `unknown`, never `fresh`.
+        return buildReport(meta, {
             isStale: false,
-            indexedAt: null,
             indexedCommit: null,
             currentCommit: null,
             changedSince: [],
             staleSince: null,
-        };
+            state: building ? 'building' : 'unknown',
+            reason: building
+                ? 'A build is currently running; git is unavailable so freshness cannot be checked.'
+                : 'Git is unavailable in this directory, so index freshness cannot be determined. Treat graph results as possibly incomplete.',
+            indexedRevision: indexedCommitFull,
+            dirty: { dirty: null, paths: [], count: null },
+        });
     }
-    // Display short SHA (7 chars) for the interface field; compare short SHAs for staleness
-    const indexedCommitShort = indexedCommitFull ? indexedCommitFull.slice(0, 7) : null;
-    const currentCommitShort = currentCommit ? currentCommit.slice(0, 7) : null;
-    // 3. If SHAs match → fresh. If no stored commit → staleness unknown (not "fresh").
+    const currentCommitShort = currentCommit.slice(0, 7);
+    const dirty = checkDirtyWorktree(repoPath);
+    // 2. Commits match → freshness still depends on worktree state and warnings.
     if (indexedCommitShort === currentCommitShort) {
-        return {
+        const { state, reason } = stateForMatchingCommit(meta, dirty);
+        return buildReport(meta, {
             isStale: false,
-            indexedAt: null,
             indexedCommit: indexedCommitShort,
             currentCommit: currentCommitShort,
             changedSince: [],
             staleSince: null,
-        };
+            state: building ? 'building' : state,
+            reason: building ? 'A build is currently running.' : reason,
+            indexedRevision: indexedCommitFull,
+            dirty,
+        });
     }
+    // 3. No recorded revision → staleness is unknown, not merely "stale".
+    //    `isStale` stays true so the rebuild guard keeps its conservative behavior.
     if (!indexedCommitFull) {
-        return {
+        return buildReport(meta, {
             isStale: true,
-            indexedAt: null,
             indexedCommit: null,
             currentCommit: currentCommitShort,
             changedSince: [],
             staleSince: null,
-        };
+            state: building ? 'building' : 'unknown',
+            reason: building
+                ? 'A build is currently running; no indexed revision has been recorded yet.'
+                : 'No indexed revision was recorded, so the index cannot be compared against HEAD.',
+            indexedRevision: null,
+            dirty,
+        });
     }
     // Guard: indexedCommitFull is read from SQLite — validate before shell interpolation
     if (!/^[0-9a-f]{7,40}$/i.test(indexedCommitFull)) {
-        return {
+        return buildReport(meta, {
             isStale: true,
-            indexedAt: null,
             indexedCommit: indexedCommitShort,
             currentCommit: currentCommitShort,
             changedSince: [],
             staleSince: null,
-        };
+            state: building ? 'building' : 'unknown',
+            reason: 'The recorded index revision is not a valid commit SHA, so freshness cannot be determined. Re-run the build.',
+            indexedRevision: indexedCommitFull,
+            dirty,
+        });
     }
     // 4. Get changed files between indexed commit and HEAD
     let changedSince = [];
@@ -75,13 +233,19 @@ export function checkStaleness(db, repoPath) {
     catch {
         staleSince = null;
     }
-    return {
+    const dirtyNote = dirty.dirty ? ` ${dirty.count} path(s) also have uncommitted changes.` : '';
+    return buildReport(meta, {
         isStale: true,
-        indexedAt: null,
         indexedCommit: indexedCommitShort,
         currentCommit: currentCommitShort,
         changedSince,
         staleSince,
-    };
+        state: building ? 'building' : 'stale',
+        reason: building
+            ? 'A build is currently running.'
+            : `Index was built at ${indexedCommitShort} but HEAD is ${currentCommitShort}; ${changedSince.length} file(s) changed since.${dirtyNote}`,
+        indexedRevision: indexedCommitFull,
+        dirty,
+    });
 }
 //# sourceMappingURL=git-staleness.js.map

package/dist/src/staleness/git-staleness.js.map

@@ -1 +1 @@
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package/dist/src/storage/fts-store.d.ts

@@ -18,6 +18,20 @@ export interface FtsResult {
     /** Last line of the symbol in its source file (1-based, null if unknown). */
     endLine: number | null;
 }
+/**
+ * THE single conversion from FTS5's `rank` to monograph's score convention.
+ *
+ * SCORE CONVENTION: every score that leaves the search layer is
+ * **higher-is-better and non-negative**. SQLite FTS5's `rank` is the opposite
+ * (negative, and *more* negative means a *better* match), so a raw rank must
+ * never escape this module — forwarding one into a ranker that takes maxima
+ * lets an unrelated node sitting at 0 outrank a genuine match at -0.656.
+ *
+ * Maps |rank| through x/(1+x) into (0, 1): monotonically increasing, so
+ * relative BM25 order is preserved, and bounded, so it composes with the
+ * additive fuzzy/node-type bonuses without one term swamping the others.
+ */
+export declare function relevanceFromFtsRank(rank: number): number;
 export declare function ftsSearch(db: Database.Database, query: string, limit: number, label?: string): FtsResult[];
 export interface HybridSearchResult extends FtsResult {
     combinedScore: number;

package/dist/src/storage/fts-store.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"fts-store.d.ts","sourceRoot":"","sources":["../../../src/storage/fts-store.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAmI3C;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAuC1D;AAED,MAAM,WAAW,SAAS;IACxB,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,GAAG,IAAI,CAAC;IACxB,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,8EAA8E;IAC9E,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,6EAA6E;IAC7E,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;CACxB;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAGzD;AAgBD,wBAAgB,SAAS,CACvB,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,KAAK,EAAE,MAAM,EACb,KAAK,EAAE,MAAM,EACb,KAAK,CAAC,EAAE,MAAM,GACb,SAAS,EAAE,CA+Jb;AAID,MAAM,WAAW,kBAAmB,SAAQ,SAAS;IACnD,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,KAAK,GAAG,MAAM,GAAG,OAAO,CAAC;CACzC;AAyCD;;;;;;;;GAQG;AACH,wBAAgB,YAAY,CAC1B,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,KAAK,EAAE,MAAM,EACb,KAAK,EAAE,MAAM,EACb,KAAK,CAAC,EAAE,MAAM,GACb,kBAAkB,EAAE,CA0EtB"}

package/dist/src/storage/fts-store.js

@@ -170,6 +170,23 @@ export function extractSearchTerms(query) {
     }
     return Array.from(terms);
 }
+/**
+ * THE single conversion from FTS5's `rank` to monograph's score convention.
+ *
+ * SCORE CONVENTION: every score that leaves the search layer is
+ * **higher-is-better and non-negative**. SQLite FTS5's `rank` is the opposite
+ * (negative, and *more* negative means a *better* match), so a raw rank must
+ * never escape this module — forwarding one into a ranker that takes maxima
+ * lets an unrelated node sitting at 0 outrank a genuine match at -0.656.
+ *
+ * Maps |rank| through x/(1+x) into (0, 1): monotonically increasing, so
+ * relative BM25 order is preserved, and bounded, so it composes with the
+ * additive fuzzy/node-type bonuses without one term swamping the others.
+ */
+export function relevanceFromFtsRank(rank) {
+    const magnitude = Math.abs(rank);
+    return magnitude / (1 + magnitude);
+}
 /**
  * Quote a single FTS5 search term as a string literal when it contains characters
  * that would otherwise be parsed as FTS5 syntax (quotes, parens, boolean keywords
@@ -391,9 +408,7 @@ export function hybridSearch(db, query, limit, label) {
     // ── Strategy 1: FTS5 BM25 ──────────────────────────────────────────────────
     const ftsRows = ftsSearch(db, safeQuery, limit * 2, label);
     for (const row of ftsRows) {
-        // FTS5 rank is negative; larger magnitude = better match. Map to (0,1) with higher = better.
-        const absRank = Math.abs(row.rank);
-        const ftsScore = absRank / (1 + absRank);
+        const ftsScore = relevanceFromFtsRank(row.rank);
         const fuzz = computeFuzzyScore(row.name, safeQuery);
         const combined = ftsScore + fuzz + computeNodeTypeBonus(row.label);
         upsert({ ...row, combinedScore: combined, matchStrategy: 'fts' });

package/dist/src/storage/fts-store.js.map

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