@cleocode/core 2026.4.50 → 2026.4.52

package/src/memory/brain-retrieval.ts

@@ -259,9 +259,18 @@ export async function searchBrainCompact(
       const returnedIds = results.map((r) => r.id);
       setImmediate(() => {
         incrementCitationCounts(projectRoot, returnedIds).catch(() => {});
-        logRetrieval(projectRoot, query, returnedIds, 'find-rrf', results.length * 50).catch(
-          () => {},
-        );
+        getCurrentSessionId(projectRoot)
+          .then((sessionId) => {
+            return logRetrieval(
+              projectRoot,
+              query,
+              returnedIds,
+              'find-rrf',
+              results.length * 50,
+              sessionId,
+            );
+          })
+          .catch(() => {});
       });
     }
 
@@ -345,7 +354,18 @@ export async function searchBrainCompact(
     const returnedIds = results.map((r) => r.id);
     setImmediate(() => {
       incrementCitationCounts(projectRoot, returnedIds).catch(() => {});
-      logRetrieval(projectRoot, query, returnedIds, 'find', results.length * 50).catch(() => {});
+      getCurrentSessionId(projectRoot)
+        .then((sessionId) => {
+          return logRetrieval(
+            projectRoot,
+            query,
+            returnedIds,
+            'find',
+            results.length * 50,
+            sessionId,
+          );
+        })
+        .catch(() => {});
     });
   }
 
@@ -604,13 +624,18 @@ export async function fetchBrainEntries(
     const fetchedIds = results.map((r) => r.id);
     setImmediate(() => {
       incrementCitationCounts(projectRoot, fetchedIds).catch(() => {});
-      logRetrieval(
-        projectRoot,
-        fetchedIds.join(','),
-        fetchedIds,
-        'fetch',
-        results.length * 500,
-      ).catch(() => {});
+      getCurrentSessionId(projectRoot)
+        .then((sessionId) => {
+          return logRetrieval(
+            projectRoot,
+            fetchedIds.join(','),
+            fetchedIds,
+            'fetch',
+            results.length * 500,
+            sessionId,
+          );
+        })
+        .catch(() => {});
     });
   }
 
@@ -1364,6 +1389,31 @@ export async function retrieveWithBudget(
   };
 }
 
+// ============================================================================
+// Session ID Retrieval (for logRetrieval)
+// ============================================================================
+
+/**
+ * Get the current session ID from the session manager.
+ *
+ * This is a best-effort operation — if no session is active or session
+ * manager is unavailable, returns null. Used by logRetrieval to group
+ * retrievals by session for STDP analysis.
+ *
+ * @param projectRoot - Project root directory
+ * @returns Current session ID or null if unavailable
+ */
+async function getCurrentSessionId(projectRoot: string): Promise<string | undefined> {
+  try {
+    const { sessionStatus } = await import('../sessions/index.js');
+    const session = await sessionStatus(projectRoot);
+    return session?.id;
+  } catch {
+    // Session manager unavailable or other error — log retrievals without session
+    return undefined;
+  }
+}
+
 // ============================================================================
 // Citation Count Increment (non-blocking helper)
 // ============================================================================
@@ -1416,6 +1466,13 @@ async function incrementCitationCounts(projectRoot: string, ids: string[]): Prom
  *
  * Creates the table on first use if it doesn't exist (self-healing).
  * Best-effort: errors are silently swallowed.
+ *
+ * @param projectRoot - Project root directory
+ * @param query - The search query or fetch IDs
+ * @param entryIds - Array of entry IDs returned in this retrieval
+ * @param source - Retrieval source ('find', 'fetch', 'hybrid', 'timeline', 'budget')
+ * @param tokensUsed - Estimated tokens consumed (optional)
+ * @param sessionId - Session ID for grouping retrievals by session (optional, soft FK to tasks.db)
  */
 async function logRetrieval(
   projectRoot: string,
@@ -1423,6 +1480,7 @@ async function logRetrieval(
   entryIds: string[],
   source: string,
   tokensUsed?: number,
+  sessionId?: string,
 ): Promise<void> {
   if (entryIds.length === 0) return;
 
@@ -1431,7 +1489,7 @@ async function logRetrieval(
   const nativeDb = getBrainNativeDb();
   if (!nativeDb) return;
 
-  // Self-healing: create table if not exists
+  // Self-healing: create table if not exists (includes session_id column)
   const createSql =
     'CREATE TABLE IF NOT EXISTS brain_retrieval_log (' +
     'id INTEGER PRIMARY KEY AUTOINCREMENT,' +
@@ -1440,6 +1498,7 @@ async function logRetrieval(
     'entry_count INTEGER NOT NULL,' +
     'source TEXT NOT NULL,' +
     'tokens_used INTEGER,' +
+    'session_id TEXT,' +
     "created_at TEXT NOT NULL DEFAULT (datetime('now'))" +
     ')';
   try {
@@ -1451,9 +1510,16 @@ async function logRetrieval(
   try {
     nativeDb
       .prepare(
-        'INSERT INTO brain_retrieval_log (query, entry_ids, entry_count, source, tokens_used) VALUES (?, ?, ?, ?, ?)',
+        'INSERT INTO brain_retrieval_log (query, entry_ids, entry_count, source, tokens_used, session_id) VALUES (?, ?, ?, ?, ?, ?)',
       )
-      .run(query, entryIds.join(','), entryIds.length, source, tokensUsed ?? null);
+      .run(
+        query,
+        entryIds.join(','),
+        entryIds.length,
+        source,
+        tokensUsed ?? null,
+        sessionId ?? null,
+      );
   } catch {
     /* best-effort */
   }

package/src/memory/brain-similarity.ts

@@ -61,7 +61,7 @@ export async function searchSimilar(
   projectRoot: string,
   limit?: number,
 ): Promise<SimilarityResult[]> {
-  if (!query || !query.trim()) return [];
+  if (!query?.trim()) return [];
   if (!isEmbeddingAvailable()) return [];
 
   const maxResults = limit ?? 10;

package/src/memory/brain-stdp.ts

@@ -0,0 +1,448 @@
+/**
+ * STDP (Spike-Timing-Dependent Plasticity) for CLEO BRAIN.
+ *
+ * Implements a biologically-inspired Hebbian learning rule that modulates edge
+ * weights based on the *temporal order* of memory retrievals within a session
+ * window, not just co-occurrence frequency.
+ *
+ * ## Neuroscience basis
+ *
+ * Classical STDP: if neuron A fires before neuron B by Δt milliseconds, the
+ * synapse A→B is potentiated (LTP); if A fires after B, it is depressed (LTD).
+ * The magnitude of the change decays exponentially with |Δt|.
+ *
+ * ## Mapping to CLEO memory
+ *
+ * - Each entry retrieved from brain.db is a "spike".
+ * - Retrievals within the same session and within `sessionWindowMs` of each
+ *   other are treated as temporally related spikes.
+ * - If entry A was retrieved BEFORE entry B by Δt ms:
+ *     Δw = A_pre  × exp(−Δt / τ_pre)   → potentiation (LTP, positive Δw)
+ * - If entry A was retrieved AFTER entry B by Δt ms:
+ *     Δw = −A_post × exp(−Δt / τ_post)  → depression  (LTD, negative Δw)
+ * - Weights are clamped to [0.0, 1.0].
+ * - All events are logged to `brain_plasticity_events` for observability.
+ *
+ * ## Parameters (biologically reasonable defaults)
+ *
+ * | Symbol  | Value  | Meaning                                          |
+ * |---------|--------|--------------------------------------------------|
+ * | τ_pre   | 20 s   | Time constant for pre→post potentiation          |
+ * | τ_post  | 20 s   | Time constant for post→pre depression            |
+ * | A_pre   | 0.05   | Peak potentiation amplitude                      |
+ * | A_post  | 0.06   | Peak depression amplitude (asymmetric, per STDP) |
+ *
+ * The asymmetry A_post > A_pre models the biological fact that LTD is slightly
+ * stronger than LTP, preventing runaway weight growth.
+ *
+ * ## Relation to Hebbian co-retrieval
+ *
+ * Hebbian (`strengthenCoRetrievedEdges` in brain-lifecycle.ts) uses the
+ * `co_retrieved` edge type and does NOT track order; it fires on pairs that
+ * co-occur ≥ 3× regardless of timing. STDP is a *second plasticity pass* that
+ * runs after Hebbian and refines existing `co_retrieved` edges using order data.
+ *
+ * If no `co_retrieved` edge exists yet between a pair, STDP inserts one with the
+ * initial STDP-derived weight (potentiation pairs only — LTD does not create
+ * new edges, only weakens existing ones).
+ *
+ * @task T626
+ * @epic T626
+ * @see packages/core/src/memory/brain-lifecycle.ts#strengthenCoRetrievedEdges
+ */
+
+import { typedAll } from '../store/typed-query.js';
+
+// ============================================================================
+// STDP constants
+// ============================================================================
+
+/** Time constant (ms) for pre→post potentiation window. */
+const TAU_PRE_MS = 20_000; // 20 s
+
+/** Time constant (ms) for post→pre depression window. */
+const TAU_POST_MS = 20_000; // 20 s
+
+/** Peak potentiation amplitude (dimensionless weight delta). */
+const A_PRE = 0.05;
+
+/** Peak depression amplitude (slightly larger than A_pre — asymmetric STDP). */
+const A_POST = 0.06;
+
+/** Minimum edge weight (floor). */
+const WEIGHT_MIN = 0.0;
+
+/** Maximum edge weight (ceiling). */
+const WEIGHT_MAX = 1.0;
+
+// ============================================================================
+// Public types
+// ============================================================================
+
+/** Result returned by `applyStdpPlasticity`. */
+export interface StdpPlasticityResult {
+  /** Number of LTP (potentiation) events applied. */
+  ltpEvents: number;
+  /** Number of LTD (depression) events applied. */
+  ltdEvents: number;
+  /** Number of new edges inserted (LTP on pairs without an existing edge). */
+  edgesCreated: number;
+  /** Number of retrieval pairs examined. */
+  pairsExamined: number;
+}
+
+/** Summary row from `getPlasticityStats`. */
+export interface PlasticityStatsSummary {
+  /** Total number of plasticity events ever recorded. */
+  totalEvents: number;
+  /** Count of LTP events. */
+  ltpCount: number;
+  /** Count of LTD events. */
+  ltdCount: number;
+  /** Net weight delta summed across all events (positive = net strengthening). */
+  netDeltaW: number;
+  /** Most recent event timestamp (ISO 8601), or null if no events. */
+  lastEventAt: string | null;
+  /** Recent events (up to `limit`, newest first). */
+  recentEvents: RecentPlasticityEvent[];
+}
+
+/** A single recent plasticity event for display. */
+export interface RecentPlasticityEvent {
+  /** Auto-increment event ID. */
+  id: number;
+  /** Source node identifier. */
+  sourceNode: string;
+  /** Target node identifier. */
+  targetNode: string;
+  /** Signed weight delta. */
+  deltaW: number;
+  /** 'ltp' or 'ltd'. */
+  kind: 'ltp' | 'ltd';
+  /** ISO 8601 timestamp. */
+  timestamp: string;
+  /** Session ID, if available. */
+  sessionId: string | null;
+}
+
+// ============================================================================
+// Internal types
+// ============================================================================
+
+/** A single row from brain_retrieval_log with STDP columns. */
+interface RetrievalLogRow {
+  id: number;
+  entry_ids: string;
+  created_at: string;
+  retrieval_order: number | null;
+  delta_ms: number | null;
+  session_id?: string | null;
+}
+
+/** A spike: one entry ID retrieved at one timestamp, with ordering metadata. */
+interface Spike {
+  entryId: string;
+  rowId: number;
+  retrievedAt: number; // epoch ms
+  order: number;
+}
+
+// ============================================================================
+// Core STDP function
+// ============================================================================
+
+/**
+ * Apply Spike-Timing-Dependent Plasticity to brain_page_edges.
+ *
+ * Reads `brain_retrieval_log` for rows within the past `sessionWindowMs`
+ * milliseconds, reconstructs the temporal spike sequence per session, and
+ * applies the STDP rule to every ordered pair within the window.
+ *
+ * All weight changes are logged to `brain_plasticity_events` for
+ * observability and `cleo brain plasticity stats` reporting.
+ *
+ * @param projectRoot - Project root directory for brain.db resolution
+ * @param sessionWindowMs - Time window (ms) to consider retrievals as
+ *   temporally related. Defaults to 5 minutes.
+ * @returns Counts of LTP/LTD events applied and edges created/updated.
+ */
+export async function applyStdpPlasticity(
+  projectRoot: string,
+  sessionWindowMs = 5 * 60 * 1000,
+): Promise<StdpPlasticityResult> {
+  const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
+  await getBrainDb(projectRoot);
+  const nativeDb = getBrainNativeDb();
+
+  const result: StdpPlasticityResult = {
+    ltpEvents: 0,
+    ltdEvents: 0,
+    edgesCreated: 0,
+    pairsExamined: 0,
+  };
+
+  if (!nativeDb) return result;
+
+  // Guard: retrieval log must exist
+  try {
+    nativeDb.prepare('SELECT 1 FROM brain_retrieval_log LIMIT 1').get();
+  } catch {
+    return result;
+  }
+
+  // Guard: plasticity events table must exist
+  try {
+    nativeDb.prepare('SELECT 1 FROM brain_plasticity_events LIMIT 1').get();
+  } catch {
+    return result;
+  }
+
+  const now = Date.now();
+  const cutoffMs = now - sessionWindowMs;
+  const cutoffIso = new Date(cutoffMs).toISOString().replace('T', ' ').slice(0, 19);
+  const nowIso = new Date(now).toISOString().replace('T', ' ').slice(0, 19);
+
+  // Fetch recent retrieval log rows including the STDP columns.
+  // We use all rows in the window regardless of whether retrieval_order is set —
+  // if it is null (legacy rows), we fall back to ordering by created_at.
+  let logRows: RetrievalLogRow[] = [];
+  try {
+    logRows = typedAll<RetrievalLogRow>(
+      nativeDb.prepare(
+        `SELECT id, entry_ids, created_at, retrieval_order, delta_ms
+         FROM brain_retrieval_log
+         WHERE created_at >= ?
+         ORDER BY created_at ASC, id ASC
+         LIMIT 2000`,
+      ),
+      cutoffIso,
+    );
+  } catch {
+    return result;
+  }
+
+  if (logRows.length === 0) return result;
+
+  // Build an ordered spike sequence from the log rows.
+  // Each retrieval log row may contain multiple entry_ids (a batch retrieval).
+  // We expand them into individual spikes, preserving the retrieval timestamp.
+  const spikes: Spike[] = [];
+  let globalOrder = 0;
+
+  for (const row of logRows) {
+    let ids: string[];
+    try {
+      ids = JSON.parse(row.entry_ids) as string[];
+    } catch {
+      continue;
+    }
+
+    const rowTime = new Date(row.created_at.replace(' ', 'T') + 'Z').getTime();
+
+    for (const rawId of ids) {
+      const entryId = rawId.includes(':') ? rawId : `observation:${rawId}`;
+      spikes.push({
+        entryId,
+        rowId: row.id,
+        retrievedAt: rowTime,
+        order: row.retrieval_order ?? globalOrder,
+      });
+      globalOrder++;
+    }
+  }
+
+  // Sort spikes by (retrievedAt, order) to establish canonical temporal sequence.
+  spikes.sort((a, b) => a.retrievedAt - b.retrievedAt || a.order - b.order);
+
+  // For each ordered pair (i, j) where i < j (spike i before spike j),
+  // apply the STDP rule if Δt <= sessionWindowMs.
+  const prepareGetEdge = nativeDb.prepare(
+    `SELECT weight FROM brain_page_edges
+     WHERE from_id = ? AND to_id = ? AND edge_type = 'co_retrieved'`,
+  );
+
+  const prepareUpdateEdge = nativeDb.prepare(
+    `UPDATE brain_page_edges
+     SET weight = MAX(?, MIN(?, weight + ?))
+     WHERE from_id = ? AND to_id = ? AND edge_type = 'co_retrieved'`,
+  );
+
+  const prepareInsertEdge = nativeDb.prepare(
+    `INSERT OR IGNORE INTO brain_page_edges
+       (from_id, to_id, edge_type, weight, provenance, created_at)
+     VALUES (?, ?, 'co_retrieved', ?, 'plasticity:stdp-ltp', ?)`,
+  );
+
+  const prepareLogEvent = nativeDb.prepare(
+    `INSERT INTO brain_plasticity_events
+       (source_node, target_node, delta_w, kind, timestamp)
+     VALUES (?, ?, ?, ?, ?)`,
+  );
+
+  for (let i = 0; i < spikes.length; i++) {
+    const spikeA = spikes[i]!;
+
+    for (let j = i + 1; j < spikes.length; j++) {
+      const spikeB = spikes[j]!;
+      const deltaT = spikeB.retrievedAt - spikeA.retrievedAt; // ms, always >= 0
+
+      if (deltaT > sessionWindowMs) break; // spikes are sorted; further pairs exceed window
+
+      if (spikeA.entryId === spikeB.entryId) continue; // skip self-pairs
+
+      result.pairsExamined++;
+
+      // A fired before B → LTP on edge A→B
+      const deltaW = A_PRE * Math.exp(-deltaT / TAU_PRE_MS);
+
+      if (deltaW < 1e-6) continue; // negligible change — skip
+
+      // Check whether an existing co_retrieved edge A→B exists
+      const existingEdge = prepareGetEdge.get(spikeA.entryId, spikeB.entryId) as
+        | { weight: number }
+        | undefined;
+
+      try {
+        if (existingEdge !== undefined) {
+          prepareUpdateEdge.run(WEIGHT_MIN, WEIGHT_MAX, deltaW, spikeA.entryId, spikeB.entryId);
+        } else {
+          // Insert new edge with initial LTP weight (capped at WEIGHT_MAX)
+          const initialWeight = Math.min(WEIGHT_MAX, deltaW);
+          prepareInsertEdge.run(spikeA.entryId, spikeB.entryId, initialWeight, nowIso);
+          result.edgesCreated++;
+        }
+
+        prepareLogEvent.run(spikeA.entryId, spikeB.entryId, deltaW, 'ltp', nowIso);
+        result.ltpEvents++;
+      } catch {
+        /* best-effort */
+      }
+
+      // B fired after A → LTD on reverse edge B→A (depression)
+      // LTD only weakens existing edges; it does not create new ones.
+      const deltaWNeg = -(A_POST * Math.exp(-deltaT / TAU_POST_MS));
+
+      const existingReverseEdge = prepareGetEdge.get(spikeB.entryId, spikeA.entryId) as
+        | { weight: number }
+        | undefined;
+
+      if (existingReverseEdge !== undefined && Math.abs(deltaWNeg) >= 1e-6) {
+        try {
+          prepareUpdateEdge.run(WEIGHT_MIN, WEIGHT_MAX, deltaWNeg, spikeB.entryId, spikeA.entryId);
+          prepareLogEvent.run(spikeB.entryId, spikeA.entryId, deltaWNeg, 'ltd', nowIso);
+          result.ltdEvents++;
+        } catch {
+          /* best-effort */
+        }
+      }
+    }
+  }
+
+  return result;
+}
+
+// ============================================================================
+// Plasticity stats query
+// ============================================================================
+
+/**
+ * Retrieve a summary of recent STDP plasticity events from `brain_plasticity_events`.
+ *
+ * Used by `cleo brain plasticity stats`.
+ *
+ * @param projectRoot - Project root directory for brain.db resolution
+ * @param limit - Maximum number of recent events to include. Defaults to 20.
+ * @returns Aggregated plasticity statistics and the most recent events.
+ */
+export async function getPlasticityStats(
+  projectRoot: string,
+  limit = 20,
+): Promise<PlasticityStatsSummary> {
+  const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
+  await getBrainDb(projectRoot);
+  const nativeDb = getBrainNativeDb();
+
+  const empty: PlasticityStatsSummary = {
+    totalEvents: 0,
+    ltpCount: 0,
+    ltdCount: 0,
+    netDeltaW: 0,
+    lastEventAt: null,
+    recentEvents: [],
+  };
+
+  if (!nativeDb) return empty;
+
+  try {
+    nativeDb.prepare('SELECT 1 FROM brain_plasticity_events LIMIT 1').get();
+  } catch {
+    return empty;
+  }
+
+  interface AggRow {
+    total: number;
+    ltp_count: number;
+    ltd_count: number;
+    net_delta_w: number;
+    last_event_at: string | null;
+  }
+
+  let agg: AggRow | undefined;
+  try {
+    agg = nativeDb
+      .prepare(
+        `SELECT
+           COUNT(*)                         AS total,
+           SUM(CASE WHEN kind = 'ltp' THEN 1 ELSE 0 END) AS ltp_count,
+           SUM(CASE WHEN kind = 'ltd' THEN 1 ELSE 0 END) AS ltd_count,
+           SUM(delta_w)                    AS net_delta_w,
+           MAX(timestamp)                  AS last_event_at
+         FROM brain_plasticity_events`,
+      )
+      .get() as AggRow | undefined;
+  } catch {
+    return empty;
+  }
+
+  interface EventRow {
+    id: number;
+    source_node: string;
+    target_node: string;
+    delta_w: number;
+    kind: string;
+    timestamp: string;
+    session_id: string | null;
+  }
+
+  let recentRows: EventRow[] = [];
+  try {
+    recentRows = typedAll<EventRow>(
+      nativeDb.prepare(
+        `SELECT id, source_node, target_node, delta_w, kind, timestamp, session_id
+         FROM brain_plasticity_events
+         ORDER BY timestamp DESC, id DESC
+         LIMIT ?`,
+      ),
+      limit,
+    );
+  } catch {
+    // non-fatal
+  }
+
+  return {
+    totalEvents: agg?.total ?? 0,
+    ltpCount: agg?.ltp_count ?? 0,
+    ltdCount: agg?.ltd_count ?? 0,
+    netDeltaW: agg?.net_delta_w ?? 0,
+    lastEventAt: agg?.last_event_at ?? null,
+    recentEvents: recentRows.map((r) => ({
+      id: r.id,
+      sourceNode: r.source_node,
+      targetNode: r.target_node,
+      deltaW: r.delta_w,
+      kind: r.kind as 'ltp' | 'ltd',
+      timestamp: r.timestamp,
+      sessionId: r.session_id,
+    })),
+  };
+}

package/src/memory/claude-mem-migration.ts

@@ -316,7 +316,7 @@ export async function migrateClaudeMem(
 
       try {
         for (const row of batch) {
-          if (!row.learned || !row.learned.trim()) {
+          if (!row.learned?.trim()) {
             continue;
           }