@cleocode/core 2026.9.8 → 2026.9.9

package/dist/memory/brain-search.js

@@ -10,6 +10,7 @@
 import { getBrainAccessor } from '../store/memory-accessor.js';
 import { typedAll } from '../store/typed-query.js';
 import { searchSimilar } from './brain-similarity.js';
+import { memoryEligibilityClause } from './eligibility.js';
 import { QUALITY_SCORE_THRESHOLD } from './quality-scoring.js';
 /** Track whether FTS5 is available in the current SQLite build. */
 let _fts5Available = null;
@@ -221,13 +222,13 @@ export async function searchBrain(projectRoot, query, options) {
     const { getBrainDb, getBrainDbPath, getBrainNativeDb } = await import('../store/memory-sqlite.js');
     await getBrainDb(projectRoot);
     const nativeDb = getBrainNativeDb(projectRoot);
-    if (!nativeDb) {
-        return { decisions: [], patterns: [], learnings: [], observations: [] };
-    }
+    if (!nativeDb)
+        throw new Error('BRAIN database unavailable during search');
     const limit = options?.limit ?? 10;
     const tables = options?.tables ?? ['decisions', 'patterns', 'learnings', 'observations'];
     const peerId = options?.peerId;
     const includeGlobal = options?.includeGlobal ?? true;
+    const includeHistory = options?.includeHistory ?? false;
     const ftsAvailable = ensureFts5Tables(nativeDb);
     if (ftsAvailable) {
         // On first search against THIS database, rebuild FTS indexes to sync any
@@ -240,9 +241,9 @@ export async function searchBrain(projectRoot, query, options) {
             _fts5RebuiltForPath = getBrainDbPath(projectRoot);
             rebuildFts5Index(nativeDb);
         }
-        return searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal);
+        return searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal, includeHistory);
     }
-    return searchWithLike(nativeDb, query, tables, limit, peerId, includeGlobal);
+    return searchWithLike(nativeDb, query, tables, limit, peerId, includeGlobal, includeHistory);
 }
 /**
  * Build a SQL peer isolation clause and the corresponding bind parameters.
@@ -273,7 +274,7 @@ function buildPeerClause(tableAlias, peerId, includeGlobal) {
 /**
  * Search using FTS5 MATCH with BM25 ranking.
  */
-function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal = true) {
+function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal = true, includeHistory = false) {
     const result = {
         decisions: [],
         patterns: [],
@@ -293,8 +294,9 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         JOIN brain_decisions d ON d.rowid = fts.rowid
         WHERE brain_decisions_fts MATCH ?
           AND (d.quality_score IS NULL OR d.quality_score >= ?)
+          ${memoryEligibilityClause('decisions', 'd', includeHistory)}
           ${clause}
-        ORDER BY bm25(brain_decisions_fts)
+        ORDER BY CASE WHEN d.decision_category = 'agent_dispatch' THEN 1 ELSE 0 END, bm25(brain_decisions_fts)
         LIMIT ?
       `);
             const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
@@ -302,7 +304,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         }
         catch {
             // FTS query failed, fall back to LIKE for this table
-            result.decisions = likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal);
+            result.decisions = likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
         }
     }
     if (tables.includes('patterns')) {
@@ -314,6 +316,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         JOIN brain_patterns p ON p.rowid = fts.rowid
         WHERE brain_patterns_fts MATCH ?
           AND (p.quality_score IS NULL OR p.quality_score >= ?)
+          ${memoryEligibilityClause('patterns', 'p', includeHistory)}
           ${clause}
         ORDER BY bm25(brain_patterns_fts)
         LIMIT ?
@@ -322,7 +325,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
             result.patterns = rows;
         }
         catch {
-            result.patterns = likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal);
+            result.patterns = likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
         }
     }
     if (tables.includes('learnings')) {
@@ -334,6 +337,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         JOIN brain_learnings l ON l.rowid = fts.rowid
         WHERE brain_learnings_fts MATCH ?
           AND (l.quality_score IS NULL OR l.quality_score >= ?)
+          ${memoryEligibilityClause('learnings', 'l', includeHistory)}
           ${clause}
         ORDER BY bm25(brain_learnings_fts)
         LIMIT ?
@@ -342,7 +346,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
             result.learnings = rows;
         }
         catch {
-            result.learnings = likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal);
+            result.learnings = likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
         }
     }
     if (tables.includes('observations')) {
@@ -354,15 +358,16 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
         JOIN brain_observations o ON o.rowid = fts.rowid
         WHERE brain_observations_fts MATCH ?
           AND (o.quality_score IS NULL OR o.quality_score >= ?)
+          ${memoryEligibilityClause('observations', 'o', includeHistory)}
           ${clause}
-        ORDER BY bm25(brain_observations_fts)
+        ORDER BY CASE WHEN o.title LIKE 'Task start:%' OR o.title LIKE 'Task complete:%' THEN 1 ELSE 0 END, bm25(brain_observations_fts)
         LIMIT ?
       `);
             const rows = matchConjunctiveFirst((matchExpr) => typedAll(stmt, matchExpr, QUALITY_SCORE_THRESHOLD, ...params, limit), fts5Queries);
             result.observations = rows;
         }
         catch {
-            result.observations = likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal);
+            result.observations = likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
         }
     }
     return result;
@@ -370,7 +375,7 @@ function searchWithFts5(nativeDb, query, tables, limit, peerId, includeGlobal =
 /**
  * Search using LIKE queries as fallback when FTS5 is unavailable.
  */
-function searchWithLike(nativeDb, query, tables, limit, peerId, includeGlobal = true) {
+function searchWithLike(nativeDb, query, tables, limit, peerId, includeGlobal = true, includeHistory = false) {
     const result = {
         decisions: [],
         patterns: [],
@@ -378,62 +383,70 @@ function searchWithLike(nativeDb, query, tables, limit, peerId, includeGlobal =
         observations: [],
     };
     if (tables.includes('decisions')) {
-        result.decisions = likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal);
+        result.decisions = likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
     }
     if (tables.includes('patterns')) {
-        result.patterns = likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal);
+        result.patterns = likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
     }
     if (tables.includes('learnings')) {
-        result.learnings = likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal);
+        result.learnings = likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
     }
     if (tables.includes('observations')) {
-        result.observations = likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal);
+        result.observations = likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal, includeHistory);
     }
     return result;
 }
-function likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal = true) {
+function likeSearchDecisions(nativeDb, query, limit, peerId, includeGlobal = true, includeHistory = false) {
     const likePattern = `%${query}%`;
     const { clause, params } = buildPeerClause('brain_decisions', peerId, includeGlobal);
+    const eligibility = memoryEligibilityClause('decisions', 'brain_decisions', includeHistory);
     return typedAll(nativeDb.prepare(`
     SELECT * FROM brain_decisions
     WHERE (decision LIKE ? OR rationale LIKE ?)
       AND (quality_score IS NULL OR quality_score >= ?)
+      ${eligibility}
       ${clause}
     ORDER BY created_at DESC
     LIMIT ?
   `), likePattern, likePattern, QUALITY_SCORE_THRESHOLD, ...params, limit);
 }
-function likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal = true) {
+function likeSearchPatterns(nativeDb, query, limit, peerId, includeGlobal = true, includeHistory = false) {
     const likePattern = `%${query}%`;
     const { clause, params } = buildPeerClause('brain_patterns', peerId, includeGlobal);
+    const eligibility = memoryEligibilityClause('patterns', 'brain_patterns', includeHistory);
     return typedAll(nativeDb.prepare(`
     SELECT * FROM brain_patterns
     WHERE (pattern LIKE ? OR context LIKE ?)
       AND (quality_score IS NULL OR quality_score >= ?)
+      ${eligibility}
       ${clause}
     ORDER BY frequency DESC
     LIMIT ?
   `), likePattern, likePattern, QUALITY_SCORE_THRESHOLD, ...params, limit);
 }
-function likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal = true) {
+function likeSearchLearnings(nativeDb, query, limit, peerId, includeGlobal = true, includeHistory = false) {
     const likePattern = `%${query}%`;
     const { clause, params } = buildPeerClause('brain_learnings', peerId, includeGlobal);
+    const eligibility = memoryEligibilityClause('learnings', 'brain_learnings', includeHistory);
     return typedAll(nativeDb.prepare(`
     SELECT * FROM brain_learnings
     WHERE (insight LIKE ? OR source LIKE ?)
       AND (quality_score IS NULL OR quality_score >= ?)
+      ${eligibility}
       ${clause}
     ORDER BY confidence DESC
     LIMIT ?
   `), likePattern, likePattern, QUALITY_SCORE_THRESHOLD, ...params, limit);
 }
-function likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal = true) {
+function likeSearchObservations(nativeDb, query, limit, peerId, includeGlobal = true, includeHistory = false) {
     const likePattern = `%${query}%`;
     const { clause, params } = buildPeerClause('brain_observations', peerId, includeGlobal);
+    const eligibility = memoryEligibilityClause('observations', 'brain_observations', includeHistory);
     return typedAll(nativeDb.prepare(`
     SELECT * FROM brain_observations
     WHERE (title LIKE ? OR narrative LIKE ?)
       AND (quality_score IS NULL OR quality_score >= ?)
+      ${eligibility}
       ${clause}
     ORDER BY created_at DESC
     LIMIT ?
@@ -694,12 +707,7 @@ export async function hybridSearch(query, projectRoot, options) {
     const includeCode = options?.includeCode ?? false;
     // --- 1. Run FTS5, vector, and code symbol search in parallel ---
     const searches = [
-        searchBrain(projectRoot, query, { limit: maxResults * 3 }).catch(() => ({
-            decisions: [],
-            patterns: [],
-            learnings: [],
-            observations: [],
-        })),
+        searchBrain(projectRoot, query, { limit: maxResults * 3 }),
         searchSimilar(query, projectRoot, maxResults * 3).catch(() => []),
     ];
     // Optionally search code symbols
@@ -811,7 +819,9 @@ export async function hybridSearch(query, projectRoot, options) {
             const neighbors = await accessor.getNeighbors(nodeId);
             for (const neighbor of neighbors) {
                 graphHits.push({
-                    id: neighbor.id,
+                    id: neighbor.id.startsWith(`${neighbor.nodeType}:`)
+                        ? neighbor.id.slice(neighbor.nodeType.length + 1)
+                        : neighbor.id,
                     type: neighbor.nodeType,
                     title: neighbor.label,
                     text: neighbor.label,
@@ -826,7 +836,27 @@ export async function hybridSearch(query, projectRoot, options) {
     }
     // --- 7. Fuse with RRF and return top-N ---
     const fused = reciprocalRankFusion(rrfSources, rrfK);
-    return fused.slice(0, maxResults).map((r) => ({
+    const { getBrainNativeDb } = await import('../store/memory-sqlite.js');
+    const nativeDb = getBrainNativeDb(projectRoot);
+    if (!nativeDb)
+        throw new Error('BRAIN database unavailable while checking retrieval eligibility');
+    const eligible = fused.filter((hit) => {
+        const table = hit.type === 'decision'
+            ? 'decisions'
+            : hit.type === 'pattern'
+                ? 'patterns'
+                : hit.type === 'learning'
+                    ? 'learnings'
+                    : hit.type === 'observation'
+                        ? 'observations'
+                        : undefined;
+        if (!table)
+            return true;
+        return (nativeDb
+            .prepare(`SELECT id FROM main.brain_${table} WHERE id = ?${memoryEligibilityClause(table)}`)
+            .get(hit.id) !== undefined);
+    });
+    return eligible.slice(0, maxResults).map((r) => ({
         id: r.id,
         score: r.rrfScore,
         type: r.type,

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

@@ -1 +1 @@
-{"version":3,"file":"brain-similarity.d.ts","sourceRoot":"","sources":["../../src/memory/brain-similarity.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAWH,MAAM,WAAW,gBAAgB;IAC/B,EAAE,EAAE,MAAM,CAAC;IACX,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;CACd;AAkBD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,aAAa,CACjC,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,MAAM,EACnB,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,gBAAgB,EAAE,CAAC,CA4G7B"}
+{"version":3,"file":"brain-similarity.d.ts","sourceRoot":"","sources":["../../src/memory/brain-similarity.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAYH,MAAM,WAAW,gBAAgB;IAC/B,EAAE,EAAE,MAAM,CAAC;IACX,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;CACd;AAkBD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,aAAa,CACjC,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,MAAM,EACnB,KAAK,CAAC,EAAE,MAAM,GACb,OAAO,CAAC,gBAAgB,EAAE,CAAC,CA4G7B"}

package/dist/memory/brain-similarity.js

@@ -11,6 +11,7 @@
 import { getBrainAccessor } from '../store/memory-accessor.js';
 import { typedAll } from '../store/typed-query.js';
 import { embedText, isEmbeddingAvailable } from './brain-embedding.js';
+import { isCurrentMemoryEntry } from './eligibility.js';
 // ============================================================================
 // ID prefix -> table type
 // ============================================================================
@@ -84,7 +85,7 @@ export async function searchSimilar(query, projectRoot, limit) {
             switch (entryType) {
                 case 'observation': {
                     const entry = await accessor.getObservation(row.id);
-                    if (entry) {
+                    if (entry && isCurrentMemoryEntry(entry)) {
                         results.push({
                             id: row.id,
                             distance: row.distance,
@@ -97,7 +98,7 @@ export async function searchSimilar(query, projectRoot, limit) {
                 }
                 case 'decision': {
                     const entry = await accessor.getDecision(row.id);
-                    if (entry) {
+                    if (entry && isCurrentMemoryEntry(entry)) {
                         results.push({
                             id: row.id,
                             distance: row.distance,
@@ -110,7 +111,7 @@ export async function searchSimilar(query, projectRoot, limit) {
                 }
                 case 'pattern': {
                     const entry = await accessor.getPattern(row.id);
-                    if (entry) {
+                    if (entry && isCurrentMemoryEntry(entry)) {
                         results.push({
                             id: row.id,
                             distance: row.distance,
@@ -123,7 +124,7 @@ export async function searchSimilar(query, projectRoot, limit) {
                 }
                 case 'learning': {
                     const entry = await accessor.getLearning(row.id);
-                    if (entry) {
+                    if (entry && isCurrentMemoryEntry(entry)) {
                         results.push({
                             id: row.id,
                             distance: row.distance,

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

@@ -1 +1 @@
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package/dist/memory/brain-stub-prune.d.ts

@@ -29,7 +29,7 @@
  *
  * Here, instead:
  *
- *   - **Dry-run is the default.** Deleting requires an explicit `apply`.
+ *   - **Dry-run is the default.** Quarantine requires an explicit `apply`.
  *   - Only OBSERVATIONS are considered. Decisions, patterns and learnings are
  *     never touched.
  *   - A row is a candidate only if it matches a named, narrow rule AND its
@@ -63,8 +63,8 @@ export interface StubPruneRule {
  * The prune rules, each narrow and independently justified.
  *
  * Every predicate is ANDed with `length(narrative) <= MAX_STUB_NARRATIVE` and
- * `verified IS NOT 1`, so no rule can reach a substantive or human-confirmed
- * record on its own.
+ * `verified IS NOT 1`. Exact empty-hook shapes establish candidacy; short
+ * narratives with additional content are retained for agent review.
  */
 export declare const STUB_PRUNE_RULES: readonly StubPruneRule[];
 /** One candidate row, for reporting. */
@@ -76,24 +76,30 @@ export interface StubPruneCandidate {
 }
 /** Outcome of a prune run. */
 export interface StubPruneResult {
-    /** Whether rows were actually deleted (`false` = dry run). */
+    /** Whether rows were actually quarantined (`false` = dry run). */
     readonly applied: boolean;
-    /** Observation count before the run. */
+    /** IDs retained in reversible quarantine by this run. */
+    readonly quarantinedIds?: readonly string[];
+    /** Invalidation timestamp needed for safe conditional restoration. */
+    readonly quarantinedAt?: string;
+    /** Active observation count before the run. */
     readonly before: number;
-    /** Observation count after (equals `before` on a dry run). */
+    /** Active observation count after (equals `before` on a dry run). */
     readonly after: number;
-    /** Number of rows matched (and deleted, when `applied`). */
+    /** Number of rows matched (and quarantined, when `applied`). */
     readonly matched: number;
+    /** All affected IDs for inspectable repair scope; sample remains limited to five. */
+    readonly candidateIds?: readonly string[];
     /** Per-rule match counts, keyed by {@link StubPruneRule.id}. */
     readonly byRule: Record<string, number>;
     /** Up to 5 example rows, so a dry run shows what would go. */
     readonly sample: readonly StubPruneCandidate[];
 }
 /**
- * Count, sample and optionally delete content-free observation stubs.
+ * Count, sample and reversibly quarantine confirmed content-free observation stubs.
  *
  * @param nativeDb - open handle to the database holding `brain_observations`.
- * @param apply - when `true`, delete the matched rows; otherwise report only.
+ * @param apply - when `true`, invalidate matched rows while retaining their content.
  * @returns counts, per-rule breakdown and a sample of matched rows.
  *
  * @example
@@ -106,4 +112,20 @@ export interface StubPruneResult {
  * @task T12073
  */
 export declare function pruneObservationStubs(nativeDb: DatabaseSync, apply: boolean): StubPruneResult;
+/**
+ * Restore only rows still bearing this quarantine receipt's timestamp.
+ * Later invalidations or edits to authority are preserved by the precondition.
+ *
+ * @param nativeDb - Canonical project database handle.
+ * @param receipt - Prior quarantine receipt with retained IDs and timestamp.
+ * @returns Count of rows restored; mismatched preconditions are left unchanged.
+ * @remarks This helper checks retained IDs and invalidation timestamps. It does
+ * not compare source-content hashes; stronger resource guards belong to the
+ * repair lifecycle. Original observation content is retained by quarantine.
+ * @example
+ * ```ts
+ * const restoredCount = restoreObservationStubs(nativeDb, quarantineReceipt);
+ * ```
+ */
+export declare function restoreObservationStubs(nativeDb: DatabaseSync, receipt: StubPruneResult): number;
 //# sourceMappingURL=brain-stub-prune.d.ts.map

package/dist/memory/brain-stub-prune.d.ts.map

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