@cleocode/core 2026.9.8 → 2026.9.9

package/dist/memory/brain-reasoning.js

@@ -12,13 +12,17 @@
  * @task T5390, T1069
  * @epic T5149, T1042
  */
+import { assessKnowledgeCoverage, KnowledgeSymbolAmbiguityError, recordKnowledgeGap, resolveKnowledgeSymbol, } from '../nexus/knowledge.js';
 import { getTaskAccessor } from '../store/data-accessor.js';
 import { getBrainAccessor } from '../store/memory-accessor.js';
 import { getBrainDb, getBrainNativeDb } from '../store/memory-sqlite.js';
+import { getNexusDb, nexusSchema } from '../store/nexus-sqlite.js';
 import { typedAll, typedGet } from '../store/typed-query.js';
 import { searchBrain } from './brain-search.js';
 import { searchSimilar } from './brain-similarity.js';
+import { isCurrentDecisionCodeEvidence } from './decision-cross-link.js';
 import { EDGE_TYPES } from './edge-types.js';
+import { graphMemoryAuthority } from './eligibility.js';
 // ============================================================================
 // Implementation
 // ============================================================================
@@ -130,12 +134,20 @@ async function findDecisionsForTask(accessor, taskId) {
  * @returns Code reason trace (never throws — empty chain on error)
  */
 export async function reasonWhySymbol(symbolId, projectRoot) {
+    const coverage = await assessKnowledgeCoverage(projectRoot);
     const emptyResult = {
+        coverage,
         symbolId,
         narrative: `No reasoning context found for symbol '${symbolId}'.`,
         chain: [],
     };
     try {
+        const graph = await getNexusDb(projectRoot);
+        const selected = resolveKnowledgeSymbol(symbolId, graph.select().from(nexusSchema.nexusNodes).all());
+        if (!selected) {
+            recordKnowledgeGap(coverage, 'missing', `No indexed symbol matches '${symbolId}'.`);
+            return emptyResult;
+        }
         await getBrainDb(projectRoot);
         const brainNative = getBrainNativeDb(projectRoot);
         if (!brainNative)
@@ -149,10 +161,10 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
         ];
         const placeholders = codeEdgeTypes.map(() => '?').join(', ');
         // 1. Find brain nodes that reference this symbol (reverse edges)
-        const reverseEdges = typedAll(brainNative.prepare(`SELECT from_id, to_id, edge_type, weight
+        const reverseEdges = typedAll(brainNative.prepare(`SELECT from_id, to_id, edge_type, weight, provenance
          FROM brain_page_edges
          WHERE to_id = ? AND edge_type IN (${placeholders})
-         LIMIT 30`), symbolId, ...codeEdgeTypes);
+         LIMIT 30`), selected.id, ...codeEdgeTypes);
         if (reverseEdges.length === 0) {
             return emptyResult;
         }
@@ -161,6 +173,8 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
         const decisionTaskIds = [];
         // 2. Walk each brain node that references this symbol
         for (const edge of reverseEdges) {
+            if (!isCurrentDecisionCodeEvidence(brainNative, edge.provenance))
+                continue;
             const brainNodeId = edge.from_id;
             if (visitedBrainIds.has(brainNodeId))
                 continue;
@@ -169,6 +183,11 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
            FROM brain_page_nodes WHERE id = ? LIMIT 1`), brainNodeId);
             if (!brainNode)
                 continue;
+            const authority = graphMemoryAuthority(brainNative, brainNode.id, brainNode.node_type);
+            if (authority === 'historical')
+                continue;
+            if (authority === 'unverified')
+                recordKnowledgeGap(coverage, 'partial', `Graph memory source is unverified: ${brainNode.id}`);
             if (brainNode.node_type === 'decision') {
                 // Fetch decision details including context_task_id
                 const decId = brainNodeId.replace(/^decision:/, '');
@@ -181,6 +200,7 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
                 }
                 chain.push({
                     type: 'decision',
+                    authority,
                     id: brainNodeId,
                     title: decRow?.decision ?? brainNode.label,
                     refs,
@@ -191,6 +211,7 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
                 const learnRow = typedGet(brainNative.prepare(`SELECT id, insight FROM brain_learnings WHERE id = ? LIMIT 1`), learnId);
                 chain.push({
                     type: 'observation',
+                    authority,
                     id: brainNodeId,
                     title: learnRow?.insight ?? brainNode.label,
                     refs: [],
@@ -199,6 +220,7 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
             else {
                 chain.push({
                     type: 'observation',
+                    authority,
                     id: brainNodeId,
                     title: brainNode.label,
                     refs: [],
@@ -240,12 +262,16 @@ export async function reasonWhySymbol(symbolId, projectRoot) {
             narrative += ` There ${observationSteps.length === 1 ? 'is' : 'are'} ${observationSteps.length} related observation${observationSteps.length === 1 ? '' : 's'}.`;
         }
         return {
+            coverage,
             symbolId,
             narrative,
             chain,
         };
     }
     catch (err) {
+        if (err instanceof KnowledgeSymbolAmbiguityError)
+            throw err;
+        recordKnowledgeGap(coverage, 'failed', err instanceof Error ? err.message : String(err));
         const msg = err instanceof Error ? err.message : String(err);
         console.warn('[brain-reasoning] reasonWhySymbol failed:', msg);
         return emptyResult;

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

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

@@ -4,8 +4,8 @@
  * T1147 Wave 7: Reconciler core module.
  *
  * Extends `runConsolidation` from brain-lifecycle with a supersession pass that
- * automatically invalidates older BRAIN entries when a newer entry contradicts
- * them with high confidence (edge weight > 0.8 on the `contradicts` graph edge).
+ * reports contradiction candidates for the calling agent. Scores do not establish
+ * authority; invalidation requires an explicit sourced replacement.
  *
  * This module absorbs the T1139 scope (decision/learning/pattern supersession)
  * and adds a scheduled `reconciler` trigger type to `brain_consolidation_events`.
@@ -13,7 +13,7 @@
  * @task T1147
  * @epic T1075
  */
-import { runConsolidation } from './brain-lifecycle.js';
+import type { RunConsolidationResult } from './brain-lifecycle.js';
 /** Options for the reconciler pass. */
 export interface ReconcilerOptions {
     /** Edge weight threshold above which a `contradicts` relationship triggers supersession. Default: 0.8 */
@@ -34,29 +34,24 @@ export interface ReconcilerResult {
         decisions: string[];
         patterns: string[];
     };
+    /** Contradiction candidates requiring sourced resolution; no authority was inferred. */
+    candidateIds?: ReconcilerResult['supersededIds'];
     /** Number of dedup/quality/promotion steps from the base consolidation pass. */
-    consolidationResult: Awaited<ReturnType<typeof runConsolidation>>;
+    consolidationResult: RunConsolidationResult;
     /** Whether this was a dry run (no writes performed on supersession pass). */
     dryRun: boolean;
 }
 /**
- * Runs the full reconciler pass for the given project.
- *
- * This is an extension of `runConsolidation` that adds a T1139 supersession
- * pass: entries whose `contradicts` edge weight exceeds `contradictionThreshold`
- * are marked `invalid_at = now()` in their respective brain tables.
- *
- * After the supersession pass, the result is logged to `brain_consolidation_events`
- * with `trigger = 'reconciler'`.
- *
- * @param projectRoot - Absolute path to the project root (used for DB location).
- * @param options     - Optional configuration overrides.
- * @returns Combined result from consolidation + supersession passes.
+ * Assess contradiction candidates for the calling agent without invoking a model.
+ * Returns empty superseded lists: replacement requires explicit sourced evidence.
+ * Optional synthesis remains available through the separate consolidation command.
  *
+ * @param projectRoot - Absolute project root.
+ * @param options - Candidate threshold, audit session, and dry-run behavior.
+ * @returns Candidates plus legacy zero-valued consolidation counters.
  * @example
- * ```typescript
- * const result = await runReconciler('/mnt/projects/myapp');
- * console.log(`Superseded: ${result.superseded}, DryRun: ${result.dryRun}`);
+ * ```ts
+ * const candidates = await runReconciler(projectRoot, { dryRun: true });
  * ```
  */
 export declare function runReconciler(projectRoot: string, options?: ReconcilerOptions): Promise<ReconcilerResult>;

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

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

@@ -4,8 +4,8 @@
  * T1147 Wave 7: Reconciler core module.
  *
  * Extends `runConsolidation` from brain-lifecycle with a supersession pass that
- * automatically invalidates older BRAIN entries when a newer entry contradicts
- * them with high confidence (edge weight > 0.8 on the `contradicts` graph edge).
+ * reports contradiction candidates for the calling agent. Scores do not establish
+ * authority; invalidation requires an explicit sourced replacement.
  *
  * This module absorbs the T1139 scope (decision/learning/pattern supersession)
  * and adds a scheduled `reconciler` trigger type to `brain_consolidation_events`.
@@ -16,23 +16,17 @@
 import { and, eq, gt, isNull } from 'drizzle-orm';
 import { getBrainDb } from '../store/memory-sqlite.js';
 import { brainConsolidationEvents, brainDecisions, brainLearnings, brainObservations, brainPageEdges, brainPatterns, } from '../store/schema/memory-schema.js';
-import { runConsolidation } from './brain-lifecycle.js';
 // ---------------------------------------------------------------------------
 // Contradiction-edge supersession
 // ---------------------------------------------------------------------------
 /**
- * Queries `brain_page_edges` for `contradicts` edges with weight above the
- * threshold and marks the *source* entry (older) as superseded by setting
- * `invalid_at = now()` on the relevant brain table.
- *
- * The edge convention is: `source → contradicts → target`, where `target` is
- * the newer/stronger entry and `source` is the one to invalidate.
+ * Find contradiction candidates without changing either record's authority.
+ * Graph scores and edge direction do not prove which source is correct.
  *
  * @param projectRoot - Absolute path to the project root.
- * @param threshold   - Edge weight threshold (default 0.8).
- * @param dryRun      - When true, returns candidates without writing.
+ * @param threshold - Minimum contradiction confidence for candidate reporting.
  */
-async function applySupersessionPass(projectRoot, threshold, dryRun) {
+async function applySupersessionPass(projectRoot, threshold) {
     const db = await getBrainDb(projectRoot);
     const supersededIds = {
         observations: [],
@@ -54,11 +48,10 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
     if (contradictEdges.length === 0) {
         return supersededIds;
     }
-    const nowIso = new Date().toISOString();
     // For each contradicts edge, attempt to supersede the source in each brain table.
     // We check each table in order; break once the source is found.
     for (const edge of contradictEdges) {
-        const sourceId = edge.sourceId;
+        const sourceId = edge.sourceId.replace(/^(observation|decision|pattern|learning):/, '');
         // Check brain_observations
         const obs = await db
             .select({ id: brainObservations.id, invalidAt: brainObservations.invalidAt })
@@ -67,13 +60,6 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
             .get();
         if (obs) {
             supersededIds.observations.push(sourceId);
-            if (!dryRun) {
-                await db
-                    .update(brainObservations)
-                    .set({ invalidAt: nowIso })
-                    .where(eq(brainObservations.id, sourceId))
-                    .run();
-            }
             continue;
         }
         // Check brain_learnings
@@ -84,13 +70,6 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
             .get();
         if (lrn) {
             supersededIds.learnings.push(sourceId);
-            if (!dryRun) {
-                await db
-                    .update(brainLearnings)
-                    .set({ invalidAt: nowIso })
-                    .where(eq(brainLearnings.id, sourceId))
-                    .run();
-            }
             continue;
         }
         // Check brain_decisions
@@ -101,13 +80,6 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
             .get();
         if (dec) {
             supersededIds.decisions.push(sourceId);
-            if (!dryRun) {
-                await db
-                    .update(brainDecisions)
-                    .set({ invalidAt: nowIso })
-                    .where(eq(brainDecisions.id, sourceId))
-                    .run();
-            }
             continue;
         }
         // Check brain_patterns
@@ -118,13 +90,6 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
             .get();
         if (pat) {
             supersededIds.patterns.push(sourceId);
-            if (!dryRun) {
-                await db
-                    .update(brainPatterns)
-                    .set({ invalidAt: nowIso })
-                    .where(eq(brainPatterns.id, sourceId))
-                    .run();
-            }
         }
     }
     return supersededIds;
@@ -133,76 +98,84 @@ async function applySupersessionPass(projectRoot, threshold, dryRun) {
 // Public API
 // ---------------------------------------------------------------------------
 /**
- * Runs the full reconciler pass for the given project.
- *
- * This is an extension of `runConsolidation` that adds a T1139 supersession
- * pass: entries whose `contradicts` edge weight exceeds `contradictionThreshold`
- * are marked `invalid_at = now()` in their respective brain tables.
- *
- * After the supersession pass, the result is logged to `brain_consolidation_events`
- * with `trigger = 'reconciler'`.
- *
- * @param projectRoot - Absolute path to the project root (used for DB location).
- * @param options     - Optional configuration overrides.
- * @returns Combined result from consolidation + supersession passes.
+ * Assess contradiction candidates for the calling agent without invoking a model.
+ * Returns empty superseded lists: replacement requires explicit sourced evidence.
+ * Optional synthesis remains available through the separate consolidation command.
  *
+ * @param projectRoot - Absolute project root.
+ * @param options - Candidate threshold, audit session, and dry-run behavior.
+ * @returns Candidates plus legacy zero-valued consolidation counters.
  * @example
- * ```typescript
- * const result = await runReconciler('/mnt/projects/myapp');
- * console.log(`Superseded: ${result.superseded}, DryRun: ${result.dryRun}`);
+ * ```ts
+ * const candidates = await runReconciler(projectRoot, { dryRun: true });
  * ```
  */
 export async function runReconciler(projectRoot, options = {}) {
     const { contradictionThreshold = 0.8, sessionId = null, dryRun = false } = options;
-    // Step 1: Run the base consolidation pass (dedup, quality recompute, tier promotion,
-    // contradiction detection, soft eviction, edge strengthening, summaries).
-    const consolidationResult = await runConsolidation(projectRoot, sessionId, 'scheduled');
-    // Step 2: Supersession pass — find contradicts edges and invalidate older entries.
-    const supersededIds = await applySupersessionPass(projectRoot, contradictionThreshold, dryRun);
+    // Repair reasoning belongs to the calling agent; optional synthesis is a separate operation.
+    const consolidationResult = {
+        deduplicated: 0,
+        qualityRecomputed: 0,
+        tierPromotions: { promoted: [], evicted: [] },
+        contradictions: 0,
+        softEvicted: 0,
+        edgesStrengthened: 0,
+        nexusEdgesStrengthened: 0,
+        summariesGenerated: 0,
+    };
+    // Step 2: Contradiction scores generate candidates, never authority mutations.
+    const candidateIds = await applySupersessionPass(projectRoot, contradictionThreshold);
+    const supersededIds = {
+        observations: [],
+        learnings: [],
+        decisions: [],
+        patterns: [],
+    };
     const superseded = supersededIds.observations.length +
         supersededIds.learnings.length +
         supersededIds.decisions.length +
         supersededIds.patterns.length;
     // Step 3: Log reconciler event to brain_consolidation_events.
     // Use best-effort (no throw) so a logging failure does not abort the reconciler.
-    try {
-        const db = await getBrainDb(projectRoot);
-        const stepResultsJson = JSON.stringify({
-            consolidation: {
-                deduplicated: consolidationResult.deduplicated,
-                qualityRecomputed: consolidationResult.qualityRecomputed,
-                contradictions: consolidationResult.contradictions,
-                softEvicted: consolidationResult.softEvicted,
-                promoted: consolidationResult.tierPromotions.promoted.length,
-                summaries: consolidationResult.summariesGenerated,
-            },
-            supersession: {
-                threshold: contradictionThreshold,
-                superseded,
-                supersededIds,
-                dryRun,
-                note: dryRun
-                    ? `dry-run: ${superseded} supersession candidates detected`
-                    : `superseded ${superseded} entries (threshold=${contradictionThreshold})`,
-            },
-        });
-        await db
-            .insert(brainConsolidationEvents)
-            .values({
-            trigger: 'reconciler',
-            sessionId: sessionId ?? null,
-            stepResultsJson,
-            succeeded: true,
-        })
-            .run();
-    }
-    catch (err) {
-        console.warn('[reconciler] Failed to log reconciler event:', err);
-    }
+    if (!dryRun)
+        try {
+            const db = await getBrainDb(projectRoot);
+            const stepResultsJson = JSON.stringify({
+                consolidation: {
+                    deduplicated: consolidationResult.deduplicated,
+                    qualityRecomputed: consolidationResult.qualityRecomputed,
+                    contradictions: consolidationResult.contradictions,
+                    softEvicted: consolidationResult.softEvicted,
+                    promoted: consolidationResult.tierPromotions.promoted.length,
+                    summaries: consolidationResult.summariesGenerated,
+                },
+                supersession: {
+                    threshold: contradictionThreshold,
+                    superseded,
+                    supersededIds,
+                    candidateIds,
+                    dryRun,
+                    note: 'Contradictions are candidates only; a calling agent must provide a sourced replacement.',
+                },
+            });
+            await db
+                .insert(brainConsolidationEvents)
+                .values({
+                trigger: 'reconciler',
+                sessionId: sessionId ?? null,
+                stepResultsJson,
+                succeeded: true,
+            })
+                .run();
+        }
+        catch (err) {
+            console.warn('[reconciler] Failed to log reconciler event:', err);
+        }
     return {
         superseded,
         supersededIds,
         consolidationResult,
+        candidateIds,
         dryRun,
     };
 }
@@ -216,7 +189,7 @@ export async function runReconciler(projectRoot, options = {}) {
  * @param contradictionThreshold - Edge weight threshold (default 0.8).
  */
 export async function countSupersessionCandidates(projectRoot, contradictionThreshold = 0.8) {
-    const ids = await applySupersessionPass(projectRoot, contradictionThreshold, true);
+    const ids = await applySupersessionPass(projectRoot, contradictionThreshold);
     return (ids.observations.length + ids.learnings.length + ids.decisions.length + ids.patterns.length);
 }
 /**

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

@@ -43,6 +43,8 @@ export interface BrainSearchOptions {
      * Defaults to true — omitting this is equivalent to `includeGlobal: true`.
      */
     includeGlobal?: boolean;
+    /** Include superseded and invalidated records for explicit historical retrieval. */
+    includeHistory?: boolean;
 }
 /**
  * Create FTS5 virtual tables and content-sync triggers if they don't exist.

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

@@ -1 +1 @@
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