@cleocode/core 2026.8.1 → 2026.8.3

package/dist/memory/brain-search.d.ts

@@ -69,6 +69,96 @@ export declare function rebuildFts5Index(nativeDb: DatabaseSync): void;
  * @task T5130
  */
 export declare function searchBrain(projectRoot: string, query: string, options?: BrainSearchOptions): Promise<BrainMemorySearchResult>;
+/**
+ * Escape special FTS5 characters in query string.
+ *
+ * Wraps each meaningful token in double quotes and joins with OR so that
+ * partial matches are returned even when some tokens are not indexable
+ * (e.g. task prefixes like "EPIC:", em-dashes "—", or short stop-words).
+ *
+ * Strategy:
+ *   1. Split on whitespace.
+ *   2. Keep only tokens that contain at least one word character (\w), which
+ *      ensures punctuation-only tokens (em dashes, colons standalone, etc.)
+ *      are dropped before they zero-out the entire result set.
+ *   3. Deduplicate case-insensitively.
+ *   4. Join with OR so the query broadens rather than requiring ALL tokens.
+ *
+ * Using AND (implicit FTS5 join) caused empty results whenever a task title
+ * contained non-word tokens such as em dashes ("—") or trailing colons
+ * ("EPIC:"), because FTS5's default tokenizer cannot index them and the
+ * AND semantics then guaranteed zero matches for the whole query. (T553 bug fix)
+ */
+export declare function escapeFts5Query(query: string): string;
+/**
+ * The two MATCH expressions used by the conjunctive-first retrieval strategy.
+ *
+ * @task T12073
+ */
+export interface Fts5QueryPair {
+    /** All terms required — high precision, may return nothing. */
+    readonly and: string;
+    /** Any term matches — high recall, used only as a fallback. */
+    readonly or: string;
+    /** Number of usable terms extracted from the query. */
+    readonly termCount: number;
+}
+/**
+ * Build the AND and OR MATCH expressions for a natural-language query.
+ *
+ * ## Why both, and why prefixes (T12073)
+ *
+ * The previous builder emitted `"tok1" OR "tok2"` — quoted terms joined by OR.
+ * Measured against the live 6,985-observation corpus, that has two failure
+ * modes that together make recall useless for anything but an exact rare token:
+ *
+ * **Quoted terms are exact, so morphological variants are invisible.** A search
+ * for `orphan` matched 113 documents; `orphan*` matched 189. Seventy-six
+ * documents saying "orphaned" or "orphans" could not be found by searching for
+ * "orphan". SQLite FTS5 has no stemmer on the `unicode61` tokenizer, so a
+ * prefix wildcard is the available substitute — and it is a good one, because
+ * it costs nothing on a prefix-indexed b-tree.
+ *
+ * **Pure OR plus BM25 ranks by term rarity, not by term coverage.** A short
+ * document matching ONE query term outranks a long one matching ALL of them,
+ * because BM25 normalises for length. On this corpus that is catastrophic:
+ * 30% of observations are sub-60-character auto-capture stubs, so the
+ * shortest, emptiest records win. Searching `nexus_symbols_fts orphan` under
+ * the old builder returned *"Consolidated: change observations (5 entries)"*
+ * as the top hit — a record with no content at all — while the conjunctive
+ * form returns only documents about orphans in nexus.
+ *
+ * So: require all terms first, and fall back to ANY only when the conjunction
+ * finds nothing. That preserves the recall the OR form was introduced for
+ * (T553: non-word tokens like em dashes zeroing out an implicit-AND query)
+ * without letting it dominate the common case.
+ *
+ * @param query - the raw user query.
+ * @returns AND/OR MATCH expressions and the usable term count.
+ *
+ * @example
+ * ```ts
+ * const q = buildFts5Queries('nexus_symbols_fts orphan');
+ * // q.and === 'nexus_symbols_fts* AND orphan*'
+ * // q.or  === 'nexus_symbols_fts* OR orphan*'
+ * ```
+ *
+ * @task T553
+ * @task T12073
+ */
+export declare function buildFts5Queries(query: string): Fts5QueryPair;
+/**
+ * Run an FTS5-backed query conjunctively, falling back to disjunctive.
+ *
+ * Single-term queries skip the fallback entirely (AND and OR are identical).
+ *
+ * @param run - executes one MATCH expression and returns its rows.
+ * @param queries - the pair from {@link buildFts5Queries}.
+ * @returns conjunctive rows when non-empty, else disjunctive rows.
+ *
+ * @task T12073
+ */
+export declare function matchConjunctiveFirst<T>(run: (matchExpr: string) => T[], queries: Fts5QueryPair): T[];
 /**
  * Reset the cached FTS5 availability flag.
  * Used in tests to force re-detection.
@@ -89,6 +179,25 @@ export interface RrfHit {
     title: string;
     text: string;
 }
+/**
+ * Round-robin interleave several independently-ranked lists.
+ *
+ * Takes rank 1 from every list, then rank 2 from every list, and so on, so a
+ * downstream consumer that scores by array position does not systematically
+ * favour whichever list happened to be concatenated first.
+ *
+ * @param lists - per-source lists, each already ordered best-first.
+ * @returns a single list preserving each source's internal order.
+ *
+ * @example
+ * ```ts
+ * interleaveRanked([['a1', 'a2'], ['b1'], ['c1', 'c2', 'c3']]);
+ * // ['a1', 'b1', 'c1', 'a2', 'c2', 'c3']
+ * ```
+ *
+ * @task T12073
+ */
+export declare function interleaveRanked<T>(lists: ReadonlyArray<readonly T[]>): T[];
 /** Fused result produced by reciprocalRankFusion. */
 export interface RrfResult {
     id: string;

package/dist/memory/brain-search.d.ts.map

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package/dist/memory/brain-search.js

@@ -195,7 +195,7 @@ export async function searchBrain(projectRoot, query, options) {
     // Ensure brain.db is initialized
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     if (!nativeDb) {
         return { decisions: [], patterns: [], learnings: [], observations: [] };
     }
@@ -251,12 +251,14 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         learnings: [],
         observations: [],
     };
-    // Escape FTS5 special characters for safety
-    const safeQuery = escapeFts5Query(query);
+    // T12073: conjunctive-first. `fts5Queries.and` requires every term (high
+    // precision); the OR form is used only when AND matches nothing, preserving
+    // the recall the disjunctive builder was introduced for (T553).
+    const fts5Queries = buildFts5Queries(query);
     if (tables.includes('decisions')) {
         const { clause, params } = buildPeerClause('d', peerId, includeGlobal);
         try {
-            const rows = typedAll(nativeDb.prepare(`
+            const stmt = nativeDb.prepare(`
         SELECT d.*
         FROM brain_decisions_fts fts
         JOIN brain_decisions d ON d.rowid = fts.rowid
@@ -265,7 +267,8 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
           ${clause}
         ORDER BY bm25(brain_decisions_fts)
         LIMIT ?
-      `), safeQuery, QUALITY_SCORE_THRESHOLD, ...params, limit);
+      `);
+            const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
             result.decisions = rows;
         }
         catch {
@@ -276,7 +279,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
     if (tables.includes('patterns')) {
         const { clause, params } = buildPeerClause('p', peerId, includeGlobal);
         try {
-            const rows = typedAll(nativeDb.prepare(`
+            const stmt = nativeDb.prepare(`
         SELECT p.*
         FROM brain_patterns_fts fts
         JOIN brain_patterns p ON p.rowid = fts.rowid
@@ -285,7 +288,8 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
           ${clause}
         ORDER BY bm25(brain_patterns_fts)
         LIMIT ?
-      `), safeQuery, QUALITY_SCORE_THRESHOLD, ...params, limit);
+      `);
+            const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
             result.patterns = rows;
         }
         catch {
@@ -295,7 +299,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
     if (tables.includes('learnings')) {
         const { clause, params } = buildPeerClause('l', peerId, includeGlobal);
         try {
-            const rows = typedAll(nativeDb.prepare(`
+            const stmt = nativeDb.prepare(`
         SELECT l.*
         FROM brain_learnings_fts fts
         JOIN brain_learnings l ON l.rowid = fts.rowid
@@ -304,7 +308,8 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
           ${clause}
         ORDER BY bm25(brain_learnings_fts)
         LIMIT ?
-      `), safeQuery, QUALITY_SCORE_THRESHOLD, ...params, limit);
+      `);
+            const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
             result.learnings = rows;
         }
         catch {
@@ -314,7 +319,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
     if (tables.includes('observations')) {
         const { clause, params } = buildPeerClause('o', peerId, includeGlobal);
         try {
-            const rows = typedAll(nativeDb.prepare(`
+            const stmt = nativeDb.prepare(`
         SELECT o.*
         FROM brain_observations_fts fts
         JOIN brain_observations o ON o.rowid = fts.rowid
@@ -323,7 +328,8 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
           ${clause}
         ORDER BY bm25(brain_observations_fts)
         LIMIT ?
-      `), safeQuery, QUALITY_SCORE_THRESHOLD, ...params, limit);
+      `);
+            const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
             result.observations = rows;
         }
         catch {
@@ -424,14 +430,56 @@ function likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal =
  * ("EPIC:"), because FTS5's default tokenizer cannot index them and the
  * AND semantics then guaranteed zero matches for the whole query. (T553 bug fix)
  */
-function escapeFts5Query(query) {
+export function escapeFts5Query(query) {
+    return buildFts5Queries(query).or;
+}
+/**
+ * Build the AND and OR MATCH expressions for a natural-language query.
+ *
+ * ## Why both, and why prefixes (T12073)
+ *
+ * The previous builder emitted `"tok1" OR "tok2"` — quoted terms joined by OR.
+ * Measured against the live 6,985-observation corpus, that has two failure
+ * modes that together make recall useless for anything but an exact rare token:
+ *
+ * **Quoted terms are exact, so morphological variants are invisible.** A search
+ * for `orphan` matched 113 documents; `orphan*` matched 189. Seventy-six
+ * documents saying "orphaned" or "orphans" could not be found by searching for
+ * "orphan". SQLite FTS5 has no stemmer on the `unicode61` tokenizer, so a
+ * prefix wildcard is the available substitute — and it is a good one, because
+ * it costs nothing on a prefix-indexed b-tree.
+ *
+ * **Pure OR plus BM25 ranks by term rarity, not by term coverage.** A short
+ * document matching ONE query term outranks a long one matching ALL of them,
+ * because BM25 normalises for length. On this corpus that is catastrophic:
+ * 30% of observations are sub-60-character auto-capture stubs, so the
+ * shortest, emptiest records win. Searching `nexus_symbols_fts orphan` under
+ * the old builder returned *"Consolidated: change observations (5 entries)"*
+ * as the top hit — a record with no content at all — while the conjunctive
+ * form returns only documents about orphans in nexus.
+ *
+ * So: require all terms first, and fall back to ANY only when the conjunction
+ * finds nothing. That preserves the recall the OR form was introduced for
+ * (T553: non-word tokens like em dashes zeroing out an implicit-AND query)
+ * without letting it dominate the common case.
+ *
+ * @param query - the raw user query.
+ * @returns AND/OR MATCH expressions and the usable term count.
+ *
+ * @example
+ * ```ts
+ * const q = buildFts5Queries('nexus_symbols_fts orphan');
+ * // q.and === 'nexus_symbols_fts* AND orphan*'
+ * // q.or  === 'nexus_symbols_fts* OR orphan*'
+ * ```
+ *
+ * @task T553
+ * @task T12073
+ */
+export function buildFts5Queries(query) {
     const rawTokens = query.trim().split(/\s+/).filter(Boolean);
-    if (rawTokens.length === 0)
-        return '""';
-    // Keep tokens that have at least one alphanumeric character and are not
-    // pure stop-words (length ≥ 2 after stripping leading/trailing punctuation).
     const seen = new Set();
-    const tokens = [];
+    const terms = [];
     for (const t of rawTokens) {
         // Strip leading/trailing non-word characters (e.g. "EPIC:" → "EPIC", "—" → "")
         const stripped = t.replace(/^\W+|\W+$/g, '');
@@ -443,12 +491,31 @@ function escapeFts5Query(query) {
         if (seen.has(lower))
             continue; // deduplicate
         seen.add(lower);
-        tokens.push(`"${stripped.replace(/"/g, '""')}"`);
+        // Quote to neutralise FTS5 syntax characters, then append the prefix
+        // operator OUTSIDE the quotes — `"foo"*` is the documented way to combine
+        // a quoted string with a prefix match.
+        terms.push(`"${stripped.replace(/"/g, '""')}"*`);
     }
-    if (tokens.length === 0)
-        return '""';
-    // OR semantics: any matching token returns the row, ranked by BM25 relevance.
-    return tokens.join(' OR ');
+    if (terms.length === 0)
+        return { and: '""', or: '""', termCount: 0 };
+    return { and: terms.join(' AND '), or: terms.join(' OR '), termCount: terms.length };
+}
+/**
+ * Run an FTS5-backed query conjunctively, falling back to disjunctive.
+ *
+ * Single-term queries skip the fallback entirely (AND and OR are identical).
+ *
+ * @param run - executes one MATCH expression and returns its rows.
+ * @param queries - the pair from {@link buildFts5Queries}.
+ * @returns conjunctive rows when non-empty, else disjunctive rows.
+ *
+ * @task T12073
+ */
+export function matchConjunctiveFirst(run, queries) {
+    const conjunctive = run(queries.and);
+    if (conjunctive.length > 0 || queries.termCount < 2)
+        return conjunctive;
+    return run(queries.or);
 }
 /**
  * Reset the cached FTS5 availability flag.
@@ -469,6 +536,36 @@ export function resetFts5Cache() {
  * standard value from Cormack, Clarke & Buettcher (SIGIR 2009).
  */
 export const RRF_K = 60;
+/**
+ * Round-robin interleave several independently-ranked lists.
+ *
+ * Takes rank 1 from every list, then rank 2 from every list, and so on, so a
+ * downstream consumer that scores by array position does not systematically
+ * favour whichever list happened to be concatenated first.
+ *
+ * @param lists - per-source lists, each already ordered best-first.
+ * @returns a single list preserving each source's internal order.
+ *
+ * @example
+ * ```ts
+ * interleaveRanked([['a1', 'a2'], ['b1'], ['c1', 'c2', 'c3']]);
+ * // ['a1', 'b1', 'c1', 'a2', 'c2', 'c3']
+ * ```
+ *
+ * @task T12073
+ */
+export function interleaveRanked(lists) {
+    const out = [];
+    const longest = lists.reduce((max, l) => Math.max(max, l.length), 0);
+    for (let i = 0; i < longest; i++) {
+        for (const list of lists) {
+            const item = list[i];
+            if (item !== undefined)
+                out.push(item);
+        }
+    }
+    return out;
+}
 /**
  * Fuse ranked lists from multiple retrieval sources using Reciprocal Rank Fusion.
  *
@@ -601,34 +698,49 @@ export async function hybridSearch(query, projectRoot, options) {
     const vecResults = allResults[1];
     const codeResults = (includeCode ? (allResults[2] ?? []) : []);
     // --- 2. Project FTS results into ranked RrfHit list ---
-    const ftsHits = [];
-    for (const d of ftsResults.decisions) {
-        ftsHits.push({
+    //
+    // T12073: INTERLEAVE the four tables instead of concatenating them.
+    //
+    // RRF scores a hit by its POSITION in this array. Concatenating
+    // decisions → patterns → learnings → observations therefore encoded a fixed
+    // precedence that has nothing to do with relevance: every decision outranked
+    // every observation, always. With 128 decisions and 6,985 observations, the
+    // largest and most recent store was structurally the least reachable —
+    // `cleo memory find "caamp marker"` returned unrelated learnings while the
+    // ONE observation matching both terms (verified by direct MATCH) never
+    // placed.
+    //
+    // Each table is already BM25-ordered internally. Round-robin interleaving
+    // preserves that intra-table ordering while removing the inter-table bias,
+    // and avoids comparing BM25 scores across separate indexes — which is not
+    // meaningful, since each has its own corpus statistics.
+    const ftsRanked = [
+        ftsResults.decisions.map((d) => ({
             id: d.id,
             type: 'decision',
             title: d.decision,
             text: `${d.decision} — ${d.rationale}`,
-        });
-    }
-    for (const p of ftsResults.patterns) {
-        ftsHits.push({
+        })),
+        ftsResults.patterns.map((p) => ({
             id: p.id,
             type: 'pattern',
             title: p.pattern,
             text: `${p.pattern} — ${p.context}`,
-        });
-    }
-    for (const l of ftsResults.learnings) {
-        ftsHits.push({
+        })),
+        ftsResults.learnings.map((l) => ({
             id: l.id,
             type: 'learning',
             title: l.insight,
             text: `${l.insight} (source: ${l.source})`,
-        });
-    }
-    for (const o of ftsResults.observations) {
-        ftsHits.push({ id: o.id, type: 'observation', title: o.title, text: o.narrative ?? o.title });
-    }
+        })),
+        ftsResults.observations.map((o) => ({
+            id: o.id,
+            type: 'observation',
+            title: o.title,
+            text: o.narrative ?? o.title,
+        })),
+    ];
+    const ftsHits = interleaveRanked(ftsRanked);
     // --- 3. Project vector results into ranked RrfHit list (ascending distance = descending quality) ---
     const vecHits = vecResults.map((r) => ({
         id: r.id,

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package/dist/memory/brain-similarity.js

@@ -55,7 +55,7 @@ export async function searchSimilar(query, projectRoot, limit) {
     // Ensure brain.db is initialized
     const { getBrainDb, getBrainNativeDb, isBrainVecLoaded } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     if (!nativeDb)
         return [];
     // Require sqlite-vec for KNN queries

package/dist/memory/brain-similarity.js.map

@@ -1 +1 @@
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package/dist/memory/brain-stdp.js

@@ -376,7 +376,7 @@ function hasMinimumRetrievalsSinceLastPlasticity(nativeDb, minCount = 2, session
 export async function shouldRunPlasticity(projectRoot, sessionId = null, minRetrievalsForPlasticity = 2) {
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     if (!nativeDb)
         return true; // Err on the side of running
     const hasMinimum = hasMinimumRetrievalsSinceLastPlasticity(nativeDb, minRetrievalsForPlasticity, sessionId);
@@ -513,7 +513,7 @@ async function applyStdpPlasticityImpl(projectRoot, options) {
     }
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     const result = {
         ltpEvents: 0,
         ltdEvents: 0,
@@ -901,7 +901,7 @@ async function applyStdpPlasticityImpl(projectRoot, options) {
 export async function getPlasticityStats(projectRoot, limit = 20) {
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     const empty = {
         totalEvents: 0,
         ltpCount: 0,
@@ -1098,7 +1098,7 @@ export async function backfillRewardSignals(projectRoot, sessionId, lookbackDays
     try {
         const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
         await getBrainDb(projectRoot);
-        const nativeDb = getBrainNativeDb();
+        const nativeDb = getBrainNativeDb(projectRoot);
         if (!nativeDb)
             return result;
         // Guard: retrieval log must exist
@@ -1208,7 +1208,7 @@ export async function applyHomeostaticDecay(projectRoot, options) {
     const result = { edgesDecayed: 0, edgesPruned: 0 };
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     if (!nativeDb)
         return result;
     // Guard: brain_page_edges must exist
@@ -1368,7 +1368,7 @@ export async function pruneStaleHistory(projectRoot, options) {
     const weightHistoryRowCap = options?.weightHistoryRowCap ?? MAX_WEIGHT_HISTORY_ROW_CAP;
     const { getBrainDb, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb();
+    const nativeDb = getBrainNativeDb(projectRoot);
     if (!nativeDb)
         return result;
     // ── Compute cutoff timestamp ──────────────────────────────────────────────