@cleocode/core 2026.4.13 → 2026.4.14

package/dist/memory/engine-compat.js

@@ -1,1397 +0,0 @@
-/**
- * Memory Engine Compatibility Layer — Brain.db Cognitive Memory
- *
- * Async wrappers around brain.db cognitive memory functions that return
- * EngineResult<T> format for consumption by the dispatch layer.
- *
- * After the memory domain cutover (T5241), this file contains ONLY
- * brain.db-backed operations. Manifest operations moved to
- * pipeline-manifest-compat.ts, and context injection moved to
- * sessions/context-inject.ts.
- *
- * @task T5241
- * @epic T5149
- */
-import { getProjectRoot } from '../paths.js';
-// BRAIN accessor for direct table queries (T5241)
-import { getBrainAccessor } from '../store/brain-accessor.js';
-import { getAccessor } from '../store/data-accessor.js';
-import { linkMemoryToTask, unlinkMemoryFromTask } from './brain-links.js';
-// BRAIN retrieval imports (T5131-T5135)
-import { fetchBrainEntries, observeBrain, searchBrainCompact, timelineBrain, } from './brain-retrieval.js';
-import { learningStats, searchLearnings, storeLearning, } from './learnings.js';
-// BRAIN memory imports (T4770)
-import { patternStats, searchPatterns, storePattern, } from './patterns.js';
-// ============================================================================
-// Internal helpers
-// ============================================================================
-function resolveRoot(projectRoot) {
-    return projectRoot || getProjectRoot();
-}
-/**
- * Parse brain.db entry ID prefix to determine the table type.
- *
- * Conventions:
- * - D... -> decision (D001, D-xxx)
- * - P... -> pattern  (P001, P-xxx)
- * - L... -> learning (L001, L-xxx)
- * - O... or CM-... -> observation (O-xxx, CM-xxx)
- */
-function parseIdPrefix(id) {
-    if (id.startsWith('D-') || /^D\d/.test(id))
-        return 'decision';
-    if (id.startsWith('P-') || /^P\d/.test(id))
-        return 'pattern';
-    if (id.startsWith('L-') || /^L\d/.test(id))
-        return 'learning';
-    if (id.startsWith('O-') || id.startsWith('O') || id.startsWith('CM-'))
-        return 'observation';
-    return null;
-}
-// ============================================================================
-// Brain.db Entry Lookup
-// ============================================================================
-/**
- * Look up a brain.db entry by ID.
- *
- * @param entryId - Brain entry ID with type prefix (D-, P-, L-, O-, or CM-)
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult containing the typed entry data on success
- *
- * @remarks
- * Parses the ID prefix to determine the entry type (decision, pattern, learning,
- * or observation) and queries the corresponding brain.db table.
- *
- * @example
- * ```typescript
- * const result = await memoryShow('O-abc123', '/project');
- * if (result.success) console.log(result.data.type, result.data.entry);
- * ```
- */
-export async function memoryShow(entryId, projectRoot) {
-    if (!entryId) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'entryId is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const entryType = parseIdPrefix(entryId);
-        if (!entryType) {
-            return {
-                success: false,
-                error: {
-                    code: 'E_INVALID_INPUT',
-                    message: `Unknown entry ID format: '${entryId}'. Expected prefix D-, P-, L-, or O-`,
-                },
-            };
-        }
-        const accessor = await getBrainAccessor(root);
-        switch (entryType) {
-            case 'decision': {
-                const row = await accessor.getDecision(entryId);
-                if (!row) {
-                    return {
-                        success: false,
-                        error: { code: 'E_NOT_FOUND', message: `Decision '${entryId}' not found in brain.db` },
-                    };
-                }
-                return { success: true, data: { type: 'decision', entry: row } };
-            }
-            case 'pattern': {
-                const row = await accessor.getPattern(entryId);
-                if (!row) {
-                    return {
-                        success: false,
-                        error: { code: 'E_NOT_FOUND', message: `Pattern '${entryId}' not found in brain.db` },
-                    };
-                }
-                return { success: true, data: { type: 'pattern', entry: row } };
-            }
-            case 'learning': {
-                const row = await accessor.getLearning(entryId);
-                if (!row) {
-                    return {
-                        success: false,
-                        error: { code: 'E_NOT_FOUND', message: `Learning '${entryId}' not found in brain.db` },
-                    };
-                }
-                return { success: true, data: { type: 'learning', entry: row } };
-            }
-            case 'observation': {
-                const row = await accessor.getObservation(entryId);
-                if (!row) {
-                    return {
-                        success: false,
-                        error: {
-                            code: 'E_NOT_FOUND',
-                            message: `Observation '${entryId}' not found in brain.db`,
-                        },
-                    };
-                }
-                return { success: true, data: { type: 'observation', entry: row } };
-            }
-        }
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_SHOW',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// Brain.db Aggregate Stats
-// ============================================================================
-/**
- * Aggregate stats from brain.db across all tables.
- *
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with observation, decision, pattern, and learning counts
- *
- * @remarks
- * Queries each brain.db table for row counts and returns a combined statistics object.
- * Returns zero counts if brain.db is not initialized.
- *
- * @example
- * ```typescript
- * const result = await memoryBrainStats('/project');
- * if (result.success) console.log(result.data.observations);
- * ```
- */
-export async function memoryBrainStats(projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
-        await getBrainDb(root);
-        const nativeDb = getBrainNativeDb();
-        if (!nativeDb) {
-            return {
-                success: true,
-                data: {
-                    observations: 0,
-                    decisions: 0,
-                    patterns: 0,
-                    learnings: 0,
-                    total: 0,
-                    message: 'brain.db not initialized',
-                },
-            };
-        }
-        const obsCount = nativeDb.prepare('SELECT COUNT(*) AS cnt FROM brain_observations').get().cnt;
-        const decCount = nativeDb.prepare('SELECT COUNT(*) AS cnt FROM brain_decisions').get().cnt;
-        const patCount = nativeDb.prepare('SELECT COUNT(*) AS cnt FROM brain_patterns').get().cnt;
-        const learnCount = nativeDb.prepare('SELECT COUNT(*) AS cnt FROM brain_learnings').get().cnt;
-        return {
-            success: true,
-            data: {
-                observations: obsCount,
-                decisions: decCount,
-                patterns: patCount,
-                learnings: learnCount,
-                total: obsCount + decCount + patCount + learnCount,
-            },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_STATS',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// Brain.db Decision Operations
-// ============================================================================
-/**
- * Search decisions in brain.db.
- *
- * @param params - Search parameters (query, limit, etc.)
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with matching decision entries
- *
- * @remarks
- * Queries the brain.db decisions table with optional text filtering and pagination.
- *
- * @example
- * ```typescript
- * const result = await memoryDecisionFind({ query: 'auth' }, '/project');
- * ```
- */
-export async function memoryDecisionFind(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        if (params.query) {
-            const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
-            await getBrainDb(root);
-            const nativeDb = getBrainNativeDb();
-            if (!nativeDb) {
-                return { success: true, data: { decisions: [], total: 0 } };
-            }
-            const likePattern = `%${params.query}%`;
-            const limit = params.limit ?? 20;
-            const rows = nativeDb
-                .prepare(`
-        SELECT * FROM brain_decisions
-        WHERE decision LIKE ? OR rationale LIKE ?
-        ORDER BY created_at DESC
-        LIMIT ?
-      `)
-                .all(likePattern, likePattern, limit);
-            return { success: true, data: { decisions: rows, total: rows.length } };
-        }
-        const decisions = await accessor.findDecisions({
-            contextTaskId: params.taskId,
-            limit: params.limit ?? 20,
-        });
-        return { success: true, data: { decisions, total: decisions.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_DECISION_FIND',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Store a decision to brain.db.
- *
- * @param params - Decision data including title, rationale, and alternatives
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the stored decision ID
- *
- * @remarks
- * Creates a new decision entry in brain.db with a D-prefixed ID.
- * Optionally refreshes the memory bridge after storing.
- *
- * @example
- * ```typescript
- * const result = await memoryDecisionStore({ title: 'Use SQLite', rationale: 'Embedded, fast' }, '/project');
- * ```
- */
-export async function memoryDecisionStore(params, projectRoot) {
-    if (!params.decision) {
-        return {
-            success: false,
-            error: { code: 'E_INVALID_INPUT', message: 'decision text is required' },
-        };
-    }
-    if (!params.rationale) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'rationale is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-        const id = `D-${Date.now().toString(36)}`;
-        const row = await accessor.addDecision({
-            id,
-            type: 'technical',
-            decision: params.decision,
-            rationale: params.rationale,
-            confidence: 'medium',
-            outcome: 'pending',
-            alternativesJson: params.alternatives ? JSON.stringify(params.alternatives) : null,
-            contextTaskId: params.taskId ?? null,
-            contextEpicId: null,
-            contextPhase: null,
-            createdAt: now,
-        });
-        return {
-            success: true,
-            data: {
-                id: row.id,
-                type: row.type,
-                decision: row.decision,
-                createdAt: row.createdAt,
-            },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_DECISION_STORE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// BRAIN Retrieval Operations (T5131-T5135) — Renamed from brain.* to flat ops
-// ============================================================================
-/**
- * Token-efficient brain search returning compact results.
- *
- * @param params - Search parameters including query string and limit
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with compact search hits (IDs and titles)
- *
- * @remarks
- * Designed for the cheapest-first retrieval pattern. Returns minimal fields
- * per hit to conserve tokens. Use memoryFetch for full entry details.
- *
- * @example
- * ```typescript
- * const result = await memoryFind({ query: 'authentication', limit: 10 }, '/project');
- * ```
- */
-export async function memoryFind(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await searchBrainCompact(root, {
-            query: params.query,
-            limit: params.limit,
-            tables: params.tables,
-            dateStart: params.dateStart,
-            dateEnd: params.dateEnd,
-        });
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_SEARCH',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Chronological context around a brain entry anchor.
- *
- * @param params - Timeline parameters including anchor ID and window size
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with chronologically ordered entries around the anchor
- *
- * @remarks
- * Retrieves entries before and after a given anchor ID for temporal context.
- * Useful for understanding the sequence of observations and decisions.
- *
- * @example
- * ```typescript
- * const result = await memoryTimeline({ anchorId: 'O-abc123', window: 5 }, '/project');
- * ```
- */
-export async function memoryTimeline(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await timelineBrain(root, {
-            anchor: params.anchor,
-            depthBefore: params.depthBefore,
-            depthAfter: params.depthAfter,
-        });
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_TIMELINE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Batch fetch brain entries by IDs.
- *
- * @param params - Fetch parameters including an array of entry IDs
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with full entry details for each requested ID
- *
- * @remarks
- * Use after memoryFind to retrieve full details for specific entries.
- * Part of the 3-layer retrieval pattern: search -> filter -> fetch.
- *
- * @example
- * ```typescript
- * const result = await memoryFetch({ ids: ['O-abc123', 'D-def456'] }, '/project');
- * ```
- */
-export async function memoryFetch(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await fetchBrainEntries(root, { ids: params.ids });
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_FETCH',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Save an observation to brain.db.
- *
- * @param params - Observation data including text, title, and optional tags
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the stored observation ID
- *
- * @remarks
- * Creates a new observation entry in brain.db with an O-prefixed ID.
- * Optionally refreshes the memory bridge after storing.
- *
- * @example
- * ```typescript
- * const result = await memoryObserve({ text: 'Auth uses JWT', title: 'Auth discovery' }, '/project');
- * ```
- */
-export async function memoryObserve(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await observeBrain(root, {
-            text: params.text,
-            title: params.title,
-            type: params.type,
-            project: params.project,
-            sourceSessionId: params.sourceSessionId,
-            sourceType: params.sourceType,
-        });
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_BRAIN_OBSERVE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// BRAIN Pattern Operations (T4770)
-// ============================================================================
-/**
- * Store a pattern to BRAIN memory.
- *
- * @param params - Pattern data including pattern string, type, and confidence
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the stored pattern ID
- *
- * @remarks
- * Persists a detected pattern (success or failure) to brain.db for future scoring.
- *
- * @example
- * ```typescript
- * const result = await memoryPatternStore({ pattern: 'migration', type: 'success' }, '/project');
- * ```
- */
-export async function memoryPatternStore(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await storePattern(root, params);
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_PATTERN_STORE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Search patterns in BRAIN memory.
- *
- * @param params - Search parameters including query and type filter
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with matching pattern entries
- *
- * @remarks
- * Queries the brain.db patterns table with optional type filtering.
- *
- * @example
- * ```typescript
- * const result = await memoryPatternFind({ type: 'success', limit: 10 }, '/project');
- * ```
- */
-export async function memoryPatternFind(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const results = await searchPatterns(root, params);
-        return { success: true, data: { patterns: results, total: results.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_PATTERN_SEARCH',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Get pattern memory statistics.
- *
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with pattern counts by type and overall totals
- *
- * @remarks
- * Aggregates pattern data from brain.db to provide type distribution and counts.
- *
- * @example
- * ```typescript
- * const result = await memoryPatternStats('/project');
- * ```
- */
-export async function memoryPatternStats(projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const stats = await patternStats(root);
-        return { success: true, data: stats };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_PATTERN_STATS',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// BRAIN Learning Operations (T4770)
-// ============================================================================
-/**
- * Store a learning to BRAIN memory.
- *
- * @param params - Learning data including text and confidence level
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the stored learning ID
- *
- * @remarks
- * Creates a new learning entry in brain.db with an L-prefixed ID.
- *
- * @example
- * ```typescript
- * const result = await memoryLearningStore({ text: 'Drizzle v1 requires beta flag' }, '/project');
- * ```
- */
-export async function memoryLearningStore(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const result = await storeLearning(root, params);
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_LEARNING_STORE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Search learnings in BRAIN memory.
- *
- * @param params - Search parameters including query and limit
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with matching learning entries
- *
- * @remarks
- * Queries the brain.db learnings table with optional text filtering.
- *
- * @example
- * ```typescript
- * const result = await memoryLearningFind({ query: 'drizzle' }, '/project');
- * ```
- */
-export async function memoryLearningFind(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const results = await searchLearnings(root, params);
-        return { success: true, data: { learnings: results, total: results.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_LEARNING_SEARCH',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Get learning memory statistics.
- *
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with learning counts and confidence distribution
- *
- * @remarks
- * Aggregates learning data from brain.db to provide totals and breakdowns.
- *
- * @example
- * ```typescript
- * const result = await memoryLearningStats('/project');
- * ```
- */
-export async function memoryLearningStats(projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const stats = await learningStats(root);
-        return { success: true, data: stats };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_LEARNING_STATS',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// BRAIN Advanced Queries & Links (T5241)
-// ============================================================================
-/**
- * Find contradictory entries in brain.db.
- *
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with pairs of contradicting observations
- *
- * @remarks
- * Scans brain.db for observations that contradict each other based on
- * semantic similarity and opposing sentiment or content.
- *
- * @example
- * ```typescript
- * const result = await memoryContradictions('/project');
- * if (result.success) console.log(result.data.contradictions);
- * ```
- */
-export async function memoryContradictions(projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
-        await getBrainDb(root);
-        const nativeDb = getBrainNativeDb();
-        if (!nativeDb) {
-            return { success: true, data: { contradictions: [] } };
-        }
-        // Negation patterns for detecting contradictions (adapted from manifest logic)
-        const negationPairs = [
-            [/\bdoes NOT\b/i, /\bdoes\b(?!.*\bnot\b)/i],
-            [/\bcannot\b/i, /\bcan\b(?!.*\bnot\b)/i],
-            [/\bno\s+\w+\s+required\b/i, /\brequired\b(?!.*\bno\b)/i],
-            [
-                /\bnot\s+(?:available|supported|possible|recommended)\b/i,
-                /\b(?:available|supported|possible|recommended)\b(?!.*\bnot\b)/i,
-            ],
-            [/\bwithout\b/i, /\brequires?\b/i],
-            [/\bavoid\b/i, /\buse\b/i],
-            [/\bdeprecated\b/i, /\brecommended\b/i],
-            [/\banti-pattern\b/i, /\bbest practice\b/i],
-        ];
-        // Fetch all decisions with context for comparison
-        const decisions = nativeDb
-            .prepare(`
-      SELECT id, type, decision, rationale, context_task_id, created_at
-      FROM brain_decisions
-      ORDER BY created_at DESC
-    `)
-            .all();
-        // Fetch all patterns
-        const patterns = nativeDb
-            .prepare(`
-      SELECT id, type, pattern, context, anti_pattern, created_at
-      FROM brain_patterns
-      ORDER BY created_at DESC
-    `)
-            .all();
-        // Fetch all learnings
-        const learnings = nativeDb
-            .prepare(`
-      SELECT id, insight, source, created_at
-      FROM brain_learnings
-      ORDER BY created_at DESC
-    `)
-            .all();
-        const contradictions = [];
-        const seenPairs = new Set();
-        // Helper to create sorted pair key
-        const pairKey = (idA, idB) => (idA < idB ? `${idA}::${idB}` : `${idB}::${idA}`);
-        // Check decisions against each other (grouped by task context)
-        const decisionsByTask = new Map();
-        for (const d of decisions) {
-            const key = d.context_task_id;
-            if (!decisionsByTask.has(key))
-                decisionsByTask.set(key, []);
-            decisionsByTask.get(key).push(d);
-        }
-        for (const [taskId, taskDecisions] of decisionsByTask) {
-            if (taskDecisions.length < 2)
-                continue;
-            for (let i = 0; i < taskDecisions.length; i++) {
-                for (let j = i + 1; j < taskDecisions.length; j++) {
-                    const a = taskDecisions[i];
-                    const b = taskDecisions[j];
-                    const key = pairKey(a.id, b.id);
-                    if (seenPairs.has(key))
-                        continue;
-                    const contentA = `${a.decision} ${a.rationale}`;
-                    const contentB = `${b.decision} ${b.rationale}`;
-                    for (const [patternNeg, patternPos] of negationPairs) {
-                        if ((patternNeg.test(contentA) && patternPos.test(contentB)) ||
-                            (patternPos.test(contentA) && patternNeg.test(contentB))) {
-                            seenPairs.add(key);
-                            contradictions.push({
-                                entryA: {
-                                    id: a.id,
-                                    type: 'decision',
-                                    content: a.decision,
-                                    createdAt: a.created_at,
-                                },
-                                entryB: {
-                                    id: b.id,
-                                    type: 'decision',
-                                    content: b.decision,
-                                    createdAt: b.created_at,
-                                },
-                                context: taskId || undefined,
-                                conflictDetails: `Negation pattern: "${contentA.slice(0, 80)}..." vs "${contentB.slice(0, 80)}..."`,
-                            });
-                            break;
-                        }
-                    }
-                }
-            }
-        }
-        // Check patterns with anti-patterns
-        for (const p of patterns) {
-            if (p.anti_pattern) {
-                contradictions.push({
-                    entryA: { id: p.id, type: 'pattern', content: p.pattern, createdAt: p.created_at },
-                    entryB: {
-                        id: p.id,
-                        type: 'anti-pattern',
-                        content: p.anti_pattern,
-                        createdAt: p.created_at,
-                    },
-                    conflictDetails: `Pattern defines its own anti-pattern`,
-                });
-            }
-        }
-        // Check learnings against each other
-        for (let i = 0; i < learnings.length; i++) {
-            for (let j = i + 1; j < learnings.length; j++) {
-                const a = learnings[i];
-                const b = learnings[j];
-                const key = pairKey(a.id, b.id);
-                if (seenPairs.has(key))
-                    continue;
-                for (const [patternNeg, patternPos] of negationPairs) {
-                    if ((patternNeg.test(a.insight) && patternPos.test(b.insight)) ||
-                        (patternPos.test(a.insight) && patternNeg.test(b.insight))) {
-                        seenPairs.add(key);
-                        contradictions.push({
-                            entryA: { id: a.id, type: 'learning', content: a.insight, createdAt: a.created_at },
-                            entryB: { id: b.id, type: 'learning', content: b.insight, createdAt: b.created_at },
-                            conflictDetails: `Learning contradiction detected`,
-                        });
-                        break;
-                    }
-                }
-            }
-        }
-        return { success: true, data: { contradictions } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_CONTRADICTIONS',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Find superseded entries in brain.db.
- *
- * Identifies entries that have been superseded by newer entries on the same topic.
- *
- * @param params - Superseded search parameters
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with superseded entry pairs and their replacements
- *
- * @remarks
- * Scans brain.db for entries where a newer observation or decision covers
- * the same topic, rendering the older entry obsolete.
- *
- * For brain.db, we group by:
- * - Decisions: type + contextTaskId/contextEpicId
- * - Patterns: type + context (first 100 chars for similarity)
- * - Learnings: source + applicableTypes
- * - Observations: type + project
- *
- * @example
- * ```typescript
- * const result = await memorySuperseded({ type: 'decision' }, '/project');
- * ```
- */
-export async function memorySuperseded(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
-        await getBrainDb(root);
-        const nativeDb = getBrainNativeDb();
-        if (!nativeDb) {
-            return { success: true, data: { superseded: [] } };
-        }
-        const superseded = [];
-        // Helper to normalize and group by key
-        const addSuperseded = (entries, groupKey) => {
-            if (entries.length < 2)
-                return;
-            // Sort by creation date (oldest first)
-            const sorted = [...entries].sort((a, b) => a.createdAt.localeCompare(b.createdAt));
-            // All but the newest are superseded by the newest
-            const newest = sorted[sorted.length - 1];
-            for (let i = 0; i < sorted.length - 1; i++) {
-                superseded.push({
-                    oldEntry: sorted[i],
-                    replacement: newest,
-                    grouping: groupKey,
-                });
-            }
-        };
-        // === DECISIONS: Group by type + contextTaskId/contextEpicId ===
-        const decisionGroups = new Map();
-        const decisionQuery = params?.type
-            ? `SELECT id, type, decision, context_task_id, context_epic_id, created_at
-          FROM brain_decisions WHERE type = ? ORDER BY created_at DESC`
-            : `SELECT id, type, decision, context_task_id, context_epic_id, created_at
-          FROM brain_decisions ORDER BY created_at DESC`;
-        const decisionParams = params?.type ? [params.type] : [];
-        const decisions = nativeDb.prepare(decisionQuery).all(...decisionParams);
-        for (const d of decisions) {
-            const contextKey = d.context_task_id || d.context_epic_id || 'general';
-            const groupKey = `decision:${d.type}:${contextKey}`;
-            if (!decisionGroups.has(groupKey))
-                decisionGroups.set(groupKey, []);
-            decisionGroups.get(groupKey).push({
-                id: d.id,
-                type: d.type,
-                createdAt: d.created_at,
-                summary: d.decision.slice(0, 100),
-            });
-        }
-        for (const [key, entries] of decisionGroups) {
-            addSuperseded(entries, key);
-        }
-        // === PATTERNS: Group by type + context (first 100 chars for similarity) ===
-        const patternGroups = new Map();
-        const patternQuery = params?.type
-            ? `SELECT id, type, pattern, context, extracted_at
-          FROM brain_patterns WHERE type = ? ORDER BY extracted_at DESC`
-            : `SELECT id, type, pattern, context, extracted_at
-          FROM brain_patterns ORDER BY extracted_at DESC`;
-        const patternParams = params?.type ? [params.type] : [];
-        const patterns = nativeDb.prepare(patternQuery).all(...patternParams);
-        for (const p of patterns) {
-            // Use first 80 chars of context as grouping key for similarity
-            const contextKey = p.context?.slice(0, 80) || 'unknown';
-            const groupKey = `pattern:${p.type}:${contextKey}`;
-            if (!patternGroups.has(groupKey))
-                patternGroups.set(groupKey, []);
-            patternGroups.get(groupKey).push({
-                id: p.id,
-                type: p.type,
-                createdAt: p.extracted_at,
-                summary: p.pattern.slice(0, 100),
-            });
-        }
-        for (const [key, entries] of patternGroups) {
-            addSuperseded(entries, key);
-        }
-        // === LEARNINGS: Group by source + applicableTypes ===
-        const learningGroups = new Map();
-        const learningQuery = `SELECT id, source, insight, applicable_types_json, created_at
-        FROM brain_learnings ORDER BY created_at DESC`;
-        const learnings = nativeDb.prepare(learningQuery).all();
-        for (const l of learnings) {
-            const applicableTypes = l.applicable_types_json
-                ? JSON.parse(l.applicable_types_json).slice(0, 2).join(',')
-                : 'general';
-            const groupKey = `learning:${l.source}:${applicableTypes}`;
-            if (!learningGroups.has(groupKey))
-                learningGroups.set(groupKey, []);
-            learningGroups.get(groupKey).push({
-                id: l.id,
-                type: 'learning',
-                createdAt: l.created_at,
-                summary: l.insight.slice(0, 100),
-            });
-        }
-        for (const [key, entries] of learningGroups) {
-            addSuperseded(entries, key);
-        }
-        // === OBSERVATIONS: Group by type + project ===
-        const observationGroups = new Map();
-        const observationQuery = params?.type
-            ? `SELECT id, type, title, project, created_at
-          FROM brain_observations WHERE type = ? ORDER BY created_at DESC`
-            : `SELECT id, type, title, project, created_at
-          FROM brain_observations ORDER BY created_at DESC`;
-        const observationParams = params?.type ? [params.type] : [];
-        const observations = nativeDb.prepare(observationQuery).all(...observationParams);
-        for (const o of observations) {
-            const projectKey = params?.project ? params.project : o.project || 'general';
-            const groupKey = `observation:${o.type}:${projectKey}`;
-            if (!observationGroups.has(groupKey))
-                observationGroups.set(groupKey, []);
-            observationGroups.get(groupKey).push({
-                id: o.id,
-                type: o.type,
-                createdAt: o.created_at,
-                summary: o.title.slice(0, 100),
-            });
-        }
-        for (const [key, entries] of observationGroups) {
-            addSuperseded(entries, key);
-        }
-        return { success: true, data: { superseded, total: superseded.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_MEMORY_SUPERSEDED',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Link a brain entry to a task.
- *
- * @param params - Link parameters including entryId and taskId
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult confirming the link was created
- *
- * @remarks
- * Creates an association between a brain.db entry and a task in tasks.db.
- * Used for traceability between memory entries and the work they relate to.
- *
- * @example
- * ```typescript
- * const result = await memoryLink({ entryId: 'O-abc123', taskId: 'T042' }, '/project');
- * ```
- */
-export async function memoryLink(params, projectRoot) {
-    if (!params.taskId || !params.entryId) {
-        return {
-            success: false,
-            error: { code: 'E_INVALID_INPUT', message: 'taskId and entryId are required' },
-        };
-    }
-    const entryType = parseIdPrefix(params.entryId);
-    if (!entryType) {
-        return {
-            success: false,
-            error: { code: 'E_INVALID_INPUT', message: 'Invalid entryId format' },
-        };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        await linkMemoryToTask(root, entryType, params.entryId, params.taskId, 'applies_to');
-        return {
-            success: true,
-            data: { linked: true, taskId: params.taskId, entryId: params.entryId },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_MEMORY_LINK',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Remove a link between a brain entry and a task.
- *
- * @param params - Unlink parameters including entryId and taskId
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult confirming the link was removed
- *
- * @remarks
- * Removes the association created by memoryLink. Idempotent if the link
- * does not exist.
- *
- * @example
- * ```typescript
- * const result = await memoryUnlink({ entryId: 'O-abc123', taskId: 'T042' }, '/project');
- * ```
- */
-export async function memoryUnlink(params, projectRoot) {
-    if (!params.taskId || !params.entryId) {
-        return {
-            success: false,
-            error: { code: 'E_INVALID_INPUT', message: 'taskId and entryId are required' },
-        };
-    }
-    const entryType = parseIdPrefix(params.entryId);
-    if (!entryType) {
-        return {
-            success: false,
-            error: { code: 'E_INVALID_INPUT', message: 'Invalid entryId format' },
-        };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        await unlinkMemoryFromTask(root, entryType, params.entryId, params.taskId, 'applies_to');
-        return {
-            success: true,
-            data: { unlinked: true, taskId: params.taskId, entryId: params.entryId },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_MEMORY_UNLINK',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// PageIndex Graph Operations (T5385)
-// ============================================================================
-/**
- * Add a node or edge to the PageIndex graph.
- *
- * @param params - Graph add parameters (node data or edge endpoints)
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult confirming the node or edge was added
- *
- * @remarks
- * Supports adding both nodes (concepts) and edges (relationships) to the
- * brain.db knowledge graph (PageIndex).
- *
- * @example
- * ```typescript
- * const result = await memoryGraphAdd({ type: 'node', label: 'auth', nodeType: 'concept' }, '/project');
- * ```
- */
-export async function memoryGraphAdd(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        // Edge mode: fromId + toId + edgeType
-        if (params.fromId && params.toId && params.edgeType) {
-            const edge = await accessor.addPageEdge({
-                fromId: params.fromId,
-                toId: params.toId,
-                edgeType: params.edgeType,
-                weight: params.weight,
-            });
-            return { success: true, data: { type: 'edge', edge } };
-        }
-        // Node mode: nodeId + nodeType + label
-        if (params.nodeId && params.nodeType && params.label) {
-            const node = await accessor.addPageNode({
-                id: params.nodeId,
-                nodeType: params.nodeType,
-                label: params.label,
-                metadataJson: params.metadataJson,
-            });
-            return { success: true, data: { type: 'node', node } };
-        }
-        return {
-            success: false,
-            error: {
-                code: 'E_INVALID_INPUT',
-                message: 'Provide (nodeId + nodeType + label) for a node or (fromId + toId + edgeType) for an edge',
-            },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_GRAPH_ADD',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Get a node and its edges from the PageIndex graph.
- *
- * @param params - Parameters including the node ID to look up
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the node data and its connected edges
- *
- * @remarks
- * Returns the full node record plus all edges where the node appears as
- * either source or target.
- *
- * @example
- * ```typescript
- * const result = await memoryGraphShow({ nodeId: 'auth' }, '/project');
- * ```
- */
-export async function memoryGraphShow(params, projectRoot) {
-    if (!params.nodeId) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'nodeId is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        const node = await accessor.getPageNode(params.nodeId);
-        if (!node) {
-            return {
-                success: false,
-                error: { code: 'E_NOT_FOUND', message: `Node '${params.nodeId}' not found` },
-            };
-        }
-        const edges = await accessor.getPageEdges(params.nodeId, 'both');
-        return { success: true, data: { node, edges } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_GRAPH_SHOW',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Get neighbor nodes from the PageIndex graph.
- *
- * @param params - Parameters including the node ID and optional depth
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with neighboring nodes and connecting edges
- *
- * @remarks
- * Traverses the knowledge graph outward from a given node to find related
- * concepts within the specified depth.
- *
- * @example
- * ```typescript
- * const result = await memoryGraphNeighbors({ nodeId: 'auth', depth: 2 }, '/project');
- * ```
- */
-export async function memoryGraphNeighbors(params, projectRoot) {
-    if (!params.nodeId) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'nodeId is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        const neighbors = await accessor.getNeighbors(params.nodeId, params.edgeType);
-        return { success: true, data: { neighbors, total: neighbors.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_GRAPH_NEIGHBORS',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-// ============================================================================
-// BRAIN Reasoning & Hybrid Search Operations (T5388-T5393)
-// ============================================================================
-/**
- * Causal trace through task dependency chains.
- *
- * @param params - Parameters including the entry or task ID to trace
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with the causal chain explaining why something happened
- *
- * @remarks
- * Traces backward through task dependencies and brain entries to build
- * an explanation chain for a given decision or observation.
- *
- * @example
- * ```typescript
- * const result = await memoryReasonWhy({ id: 'D-abc123' }, '/project');
- * ```
- */
-export async function memoryReasonWhy(params, projectRoot) {
-    if (!params.taskId) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'taskId is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const taskAccessor = await getAccessor(root);
-        const { reasonWhy } = await import('./brain-reasoning.js');
-        const result = await reasonWhy(params.taskId, root, taskAccessor);
-        return { success: true, data: result };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_REASON_WHY',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Find semantically similar entries.
- *
- * @param params - Parameters including the source entry ID or query text
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with entries ranked by semantic similarity
- *
- * @remarks
- * Uses embedding vectors or text similarity to find brain entries that are
- * semantically close to the given reference.
- *
- * @example
- * ```typescript
- * const result = await memoryReasonSimilar({ id: 'O-abc123', limit: 5 }, '/project');
- * ```
- */
-export async function memoryReasonSimilar(params, projectRoot) {
-    if (!params.entryId) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'entryId is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const { reasonSimilar } = await import('./brain-reasoning.js');
-        const results = await reasonSimilar(params.entryId, root, params.limit);
-        return { success: true, data: { results, total: results.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_REASON_SIMILAR',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Hybrid search across FTS5, vector, and graph.
- *
- * @param params - Search parameters including query and optional mode/limit
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult with merged and ranked results from all search backends
- *
- * @remarks
- * Combines full-text search (FTS5), vector similarity, and graph traversal
- * to produce comprehensive search results with merged relevance scoring.
- *
- * @example
- * ```typescript
- * const result = await memorySearchHybrid({ query: 'authentication flow' }, '/project');
- * ```
- */
-export async function memorySearchHybrid(params, projectRoot) {
-    if (!params.query) {
-        return { success: false, error: { code: 'E_INVALID_INPUT', message: 'query is required' } };
-    }
-    try {
-        const root = resolveRoot(projectRoot);
-        const { hybridSearch } = await import('./brain-search.js');
-        const results = await hybridSearch(params.query, root, {
-            ftsWeight: params.ftsWeight,
-            vecWeight: params.vecWeight,
-            graphWeight: params.graphWeight,
-            limit: params.limit,
-        });
-        return { success: true, data: { results, total: results.length } };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_HYBRID_SEARCH',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-/**
- * Remove a node or edge from the PageIndex graph.
- *
- * @param params - Parameters specifying the node or edge to remove
- * @param projectRoot - Optional project root path; defaults to resolved root
- * @returns EngineResult confirming the removal
- *
- * @remarks
- * Removes a node (and its connected edges) or a specific edge from the
- * brain.db knowledge graph.
- *
- * @example
- * ```typescript
- * const result = await memoryGraphRemove({ type: 'node', nodeId: 'stale-concept' }, '/project');
- * ```
- */
-export async function memoryGraphRemove(params, projectRoot) {
-    try {
-        const root = resolveRoot(projectRoot);
-        const accessor = await getBrainAccessor(root);
-        // Edge removal: fromId + toId + edgeType
-        if (params.fromId && params.toId && params.edgeType) {
-            await accessor.removePageEdge(params.fromId, params.toId, params.edgeType);
-            return {
-                success: true,
-                data: {
-                    removed: 'edge',
-                    fromId: params.fromId,
-                    toId: params.toId,
-                    edgeType: params.edgeType,
-                },
-            };
-        }
-        // Node removal: nodeId (cascades edges)
-        if (params.nodeId) {
-            await accessor.removePageNode(params.nodeId);
-            return { success: true, data: { removed: 'node', nodeId: params.nodeId } };
-        }
-        return {
-            success: false,
-            error: {
-                code: 'E_INVALID_INPUT',
-                message: 'Provide nodeId to remove a node or (fromId + toId + edgeType) to remove an edge',
-            },
-        };
-    }
-    catch (error) {
-        return {
-            success: false,
-            error: {
-                code: 'E_GRAPH_REMOVE',
-                message: error instanceof Error ? error.message : String(error),
-            },
-        };
-    }
-}
-//# sourceMappingURL=engine-compat.js.map