@cleocode/core 2026.4.7 → 2026.4.11

package/dist/memory/brain-lifecycle.js

@@ -0,0 +1,298 @@
+/**
+ * BRAIN lifecycle operations — temporal decay and memory consolidation.
+ *
+ * Reduces confidence of stale learnings based on age, following an
+ * exponential decay model: new_confidence = confidence * (decayRate ^ daysSinceUpdate).
+ *
+ * Consolidation groups old observations by keyword overlap and merges
+ * clusters into summary observations, archiving the originals.
+ *
+ * @task T5394 T5395
+ * @epic T5149
+ */
+import { createHash } from 'node:crypto';
+import { getBrainAccessor } from '../store/brain-accessor.js';
+import { typedAll } from '../store/typed-query.js';
+/**
+ * Apply temporal decay to brain_learnings confidence values.
+ *
+ * Entries older than `olderThanDays` have their confidence reduced
+ * by an exponential decay factor based on the number of days since
+ * their last update (or creation if never updated).
+ *
+ * Formula: new_confidence = confidence * (decayRate ^ daysSinceUpdate)
+ *
+ * @param projectRoot - Project root directory for brain.db resolution
+ * @param options - Decay configuration
+ * @returns Count of updated rows and tables processed
+ */
+export async function applyTemporalDecay(projectRoot, options) {
+    const decayRate = options?.decayRate ?? 0.995;
+    const olderThanDays = options?.olderThanDays ?? 30;
+    // Ensure brain.db is initialized
+    const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
+    await getBrainDb(projectRoot);
+    const nativeDb = getBrainNativeDb();
+    if (!nativeDb) {
+        return { updated: 0, tablesProcessed: [] };
+    }
+    // Calculate the cutoff date
+    const cutoffDate = new Date(Date.now() - olderThanDays * 24 * 60 * 60 * 1000)
+        .toISOString()
+        .replace('T', ' ')
+        .slice(0, 19);
+    // Update learnings: reduce confidence based on age since last update (or creation).
+    // SQLite's julianday function computes the difference in days.
+    // We use COALESCE to prefer updated_at over created_at for the age calculation.
+    const stmt = nativeDb.prepare(`
+    UPDATE brain_learnings
+    SET confidence = confidence * POWER(?, julianday('now') - julianday(COALESCE(updated_at, created_at))),
+        updated_at = datetime('now')
+    WHERE COALESCE(updated_at, created_at) < ?
+      AND confidence > 0.01
+  `);
+    const result = stmt.run(decayRate, cutoffDate);
+    const updated = typeof result.changes === 'number' ? result.changes : 0;
+    return {
+        updated,
+        tablesProcessed: ['brain_learnings'],
+    };
+}
+/** Stop words excluded from keyword extraction. */
+const STOP_WORDS = new Set([
+    'the',
+    'a',
+    'an',
+    'is',
+    'are',
+    'was',
+    'were',
+    'be',
+    'been',
+    'being',
+    'have',
+    'has',
+    'had',
+    'do',
+    'does',
+    'did',
+    'will',
+    'would',
+    'could',
+    'should',
+    'may',
+    'might',
+    'shall',
+    'can',
+    'need',
+    'dare',
+    'ought',
+    'used',
+    'to',
+    'of',
+    'in',
+    'for',
+    'on',
+    'with',
+    'at',
+    'by',
+    'from',
+    'as',
+    'into',
+    'through',
+    'during',
+    'before',
+    'after',
+    'above',
+    'below',
+    'between',
+    'out',
+    'off',
+    'over',
+    'under',
+    'again',
+    'further',
+    'then',
+    'once',
+    'and',
+    'but',
+    'or',
+    'nor',
+    'not',
+    'so',
+    'yet',
+    'both',
+    'either',
+    'neither',
+    'each',
+    'every',
+    'all',
+    'any',
+    'few',
+    'more',
+    'most',
+    'other',
+    'some',
+    'such',
+    'no',
+    'only',
+    'own',
+    'same',
+    'than',
+    'too',
+    'very',
+    'just',
+    'because',
+    'until',
+    'while',
+    'about',
+    'against',
+    'this',
+    'that',
+    'these',
+    'those',
+    'it',
+    'its',
+]);
+/**
+ * Extract significant keywords from text for grouping.
+ * Filters stop words and short tokens, returns lowercase words.
+ */
+function extractKeywords(text) {
+    const words = text
+        .toLowerCase()
+        .replace(/[^a-z0-9\s-]/g, '')
+        .split(/\s+/);
+    const keywords = new Set();
+    for (const w of words) {
+        if (w.length >= 4 && !STOP_WORDS.has(w)) {
+            keywords.add(w);
+        }
+    }
+    return keywords;
+}
+/**
+ * Calculate keyword overlap ratio between two sets.
+ * Returns the Jaccard similarity coefficient.
+ */
+function keywordOverlap(a, b) {
+    if (a.size === 0 || b.size === 0)
+        return 0;
+    let intersection = 0;
+    for (const w of a) {
+        if (b.has(w))
+            intersection++;
+    }
+    const union = a.size + b.size - intersection;
+    return union > 0 ? intersection / union : 0;
+}
+/**
+ * Consolidate old observations by keyword similarity.
+ *
+ * Groups observations older than `olderThanDays` by FTS5 keyword overlap.
+ * For groups with at least `minClusterSize` entries, creates one summary
+ * observation and marks originals as archived (updated_at set, narrative
+ * prefixed with [ARCHIVED]).
+ *
+ * @param projectRoot - Project root directory for brain.db resolution
+ * @param options - Consolidation configuration
+ * @returns Counts of grouped, merged, and archived observations
+ */
+export async function consolidateMemories(projectRoot, options) {
+    const olderThanDays = options?.olderThanDays ?? 90;
+    const minClusterSize = options?.minClusterSize ?? 3;
+    const { getBrainDb, getBrainNativeDb } = await import('../store/brain-sqlite.js');
+    await getBrainDb(projectRoot);
+    const nativeDb = getBrainNativeDb();
+    if (!nativeDb) {
+        return { grouped: 0, merged: 0, archived: 0 };
+    }
+    const cutoffDate = new Date(Date.now() - olderThanDays * 24 * 60 * 60 * 1000)
+        .toISOString()
+        .replace('T', ' ')
+        .slice(0, 19);
+    // Fetch old observations that are not already archived
+    const stmt = nativeDb.prepare(`
+    SELECT id, type, title, narrative, project, created_at
+    FROM brain_observations
+    WHERE created_at < ?
+      AND narrative NOT LIKE '[ARCHIVED]%'
+    ORDER BY created_at DESC
+  `);
+    const oldObservations = typedAll(stmt, cutoffDate);
+    if (oldObservations.length < minClusterSize) {
+        return { grouped: 0, merged: 0, archived: 0 };
+    }
+    // Extract keywords for each observation
+    const entries = oldObservations.map((obs) => ({
+        ...obs,
+        keywords: extractKeywords(`${obs.title} ${obs.narrative ?? ''}`),
+        clustered: false,
+    }));
+    // Greedy clustering: group by keyword overlap >= 0.3
+    const clusters = [];
+    const overlapThreshold = 0.3;
+    for (let i = 0; i < entries.length; i++) {
+        if (entries[i].clustered)
+            continue;
+        const cluster = [entries[i]];
+        entries[i].clustered = true;
+        for (let j = i + 1; j < entries.length; j++) {
+            if (entries[j].clustered)
+                continue;
+            if (entries[i].type !== entries[j].type)
+                continue;
+            const overlap = keywordOverlap(entries[i].keywords, entries[j].keywords);
+            if (overlap >= overlapThreshold) {
+                cluster.push(entries[j]);
+                entries[j].clustered = true;
+            }
+        }
+        if (cluster.length >= minClusterSize) {
+            clusters.push(cluster);
+        }
+    }
+    let grouped = 0;
+    let merged = 0;
+    let archived = 0;
+    const accessor = await getBrainAccessor(projectRoot);
+    const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
+    for (const cluster of clusters) {
+        grouped += cluster.length;
+        // Create summary observation from cluster
+        const titles = cluster.map((c) => c.title).join('; ');
+        const summaryTitle = `Consolidated: ${cluster[0].type} observations (${cluster.length} entries)`;
+        const summaryNarrative = `Merged from ${cluster.length} observations: ${titles.slice(0, 500)}`;
+        const contentHash = createHash('sha256')
+            .update(summaryTitle + summaryNarrative)
+            .digest('hex')
+            .slice(0, 16);
+        const id = `O-${Date.now().toString(36)}`;
+        await accessor.addObservation({
+            id,
+            type: cluster[0]
+                .type,
+            title: summaryTitle,
+            narrative: summaryNarrative,
+            contentHash,
+            project: cluster[0].project ?? null,
+            sourceType: 'agent',
+            createdAt: now,
+        });
+        merged++;
+        // Archive originals by prefixing narrative
+        for (const obs of cluster) {
+            nativeDb
+                .prepare(`
+        UPDATE brain_observations
+        SET narrative = '[ARCHIVED] ' || COALESCE(narrative, ''),
+            updated_at = ?
+        WHERE id = ?
+      `)
+                .run(now, obs.id);
+            archived++;
+        }
+    }
+    return { grouped, merged, archived };
+}
+//# sourceMappingURL=brain-lifecycle.js.map

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

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package/dist/memory/brain-links.js

@@ -0,0 +1,161 @@
+/**
+ * Cross-reference management between BRAIN memory entries and tasks.
+ *
+ * Provides linking/unlinking and query functions for relationships
+ * between decisions, patterns, learnings and CLEO tasks.
+ *
+ * @task T5156
+ * @epic T5149
+ */
+import { getBrainAccessor } from '../store/brain-accessor.js';
+import { taskExistsInTasksDb } from '../store/cross-db-cleanup.js';
+import { getDb } from '../store/sqlite.js';
+/**
+ * Link a memory entry to a task.
+ *
+ * @task T5156
+ */
+export async function linkMemoryToTask(projectRoot, memoryType, memoryId, taskId, linkType) {
+    if (!memoryId || !taskId) {
+        throw new Error('memoryId and taskId are required');
+    }
+    // Write-guard: reject stale task IDs before creating cross-db reference
+    const tasksDb = await getDb(projectRoot);
+    if (!(await taskExistsInTasksDb(taskId, tasksDb))) {
+        throw new Error(`Write-guard: task ${taskId} does not exist in tasks.db — refusing to create brain link`);
+    }
+    const accessor = await getBrainAccessor(projectRoot);
+    // Check if link already exists
+    const existingLinks = await accessor.getLinksForMemory(memoryType, memoryId);
+    const duplicate = existingLinks.find((l) => l.taskId === taskId && l.linkType === linkType);
+    if (duplicate) {
+        return duplicate;
+    }
+    await accessor.addLink({
+        memoryType,
+        memoryId,
+        taskId,
+        linkType,
+    });
+    // Return the created link
+    const links = await accessor.getLinksForMemory(memoryType, memoryId);
+    return links.find((l) => l.taskId === taskId && l.linkType === linkType);
+}
+/**
+ * Remove a link between a memory entry and a task.
+ *
+ * @task T5156
+ */
+export async function unlinkMemoryFromTask(projectRoot, memoryType, memoryId, taskId, linkType) {
+    const accessor = await getBrainAccessor(projectRoot);
+    await accessor.removeLink(memoryType, memoryId, taskId, linkType);
+}
+/**
+ * Get all memory entries linked to a specific task.
+ *
+ * @task T5156
+ */
+export async function getTaskLinks(projectRoot, taskId) {
+    const accessor = await getBrainAccessor(projectRoot);
+    return accessor.getLinksForTask(taskId);
+}
+/**
+ * Get all tasks linked to a specific memory entry.
+ *
+ * @task T5156
+ */
+export async function getMemoryLinks(projectRoot, memoryType, memoryId) {
+    const accessor = await getBrainAccessor(projectRoot);
+    return accessor.getLinksForMemory(memoryType, memoryId);
+}
+/**
+ * Batch create multiple links at once.
+ *
+ * @task T5156
+ */
+export async function bulkLink(projectRoot, links) {
+    const accessor = await getBrainAccessor(projectRoot);
+    const tasksDb = await getDb(projectRoot);
+    let created = 0;
+    let skipped = 0;
+    for (const link of links) {
+        // Write-guard: reject stale task IDs before creating cross-db reference
+        if (!(await taskExistsInTasksDb(link.taskId, tasksDb))) {
+            skipped++;
+            continue;
+        }
+        // Check for duplicate
+        const existing = await accessor.getLinksForMemory(link.memoryType, link.memoryId);
+        const duplicate = existing.find((l) => l.taskId === link.taskId && l.linkType === link.linkType);
+        if (duplicate) {
+            skipped++;
+            continue;
+        }
+        await accessor.addLink({
+            memoryType: link.memoryType,
+            memoryId: link.memoryId,
+            taskId: link.taskId,
+            linkType: link.linkType,
+        });
+        created++;
+    }
+    return { created, skipped };
+}
+/**
+ * Get all decisions linked to a task.
+ * Convenience method that fetches full decision rows.
+ *
+ * @task T5156
+ */
+export async function getLinkedDecisions(projectRoot, taskId) {
+    const accessor = await getBrainAccessor(projectRoot);
+    const links = await accessor.getLinksForTask(taskId);
+    const decisionLinks = links.filter((l) => l.memoryType === 'decision');
+    const decisions = [];
+    for (const link of decisionLinks) {
+        const decision = await accessor.getDecision(link.memoryId);
+        if (decision) {
+            decisions.push(decision);
+        }
+    }
+    return decisions;
+}
+/**
+ * Get all patterns linked to a task.
+ * Convenience method that fetches full pattern rows.
+ *
+ * @task T5156
+ */
+export async function getLinkedPatterns(projectRoot, taskId) {
+    const accessor = await getBrainAccessor(projectRoot);
+    const links = await accessor.getLinksForTask(taskId);
+    const patternLinks = links.filter((l) => l.memoryType === 'pattern');
+    const patterns = [];
+    for (const link of patternLinks) {
+        const pattern = await accessor.getPattern(link.memoryId);
+        if (pattern) {
+            patterns.push(pattern);
+        }
+    }
+    return patterns;
+}
+/**
+ * Get all learnings linked to a task.
+ * Convenience method that fetches full learning rows.
+ *
+ * @task T5156
+ */
+export async function getLinkedLearnings(projectRoot, taskId) {
+    const accessor = await getBrainAccessor(projectRoot);
+    const links = await accessor.getLinksForTask(taskId);
+    const learningLinks = links.filter((l) => l.memoryType === 'learning');
+    const learnings = [];
+    for (const link of learningLinks) {
+        const learning = await accessor.getLearning(link.memoryId);
+        if (learning) {
+            learnings.push(learning);
+        }
+    }
+    return learnings;
+}
+//# sourceMappingURL=brain-links.js.map

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

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package/dist/memory/brain-maintenance.js

@@ -0,0 +1,114 @@
+/**
+ * Brain Maintenance Runner
+ *
+ * Combines temporal decay, memory consolidation, and embedding backfill
+ * into a single idempotent maintenance pass. Designed to be run on a
+ * schedule or on-demand via `cleo brain maintenance`.
+ *
+ * Steps run in order:
+ *   1. Temporal decay   — reduce confidence of stale learnings
+ *   2. Consolidation    — merge duplicate/similar old observations
+ *   3. Embedding backfill — populate vectors for observations without them
+ *
+ * Each step is individually opt-outable via skip flags, making the
+ * operation safe to re-run at any frequency.
+ *
+ * @task T143
+ * @epic T134
+ * @why Enable scheduled brain optimization via single command
+ * @what Combined maintenance runner with CLI command and progress reporting
+ */
+import { reconcileOrphanedRefs } from '../store/cross-db-cleanup.js';
+import { applyTemporalDecay, consolidateMemories } from './brain-lifecycle.js';
+import { populateEmbeddings } from './brain-retrieval.js';
+// ============================================================================
+// Runner
+// ============================================================================
+/**
+ * Run a combined brain maintenance pass: decay, consolidation, and embeddings.
+ *
+ * The three steps always run in the same order:
+ *   1. `applyTemporalDecay` — decay stale learning confidence values
+ *   2. `consolidateMemories` — merge clustered old observations
+ *   3. `populateEmbeddings` — backfill missing vectors
+ *
+ * Each step is optional via the `skip*` flags. The function is idempotent:
+ * re-running it when there is nothing to process returns zero counts.
+ *
+ * @param projectRoot - Absolute path to the project root (used to locate brain.db)
+ * @param options - Optional skip flags and progress callback
+ * @returns Aggregated counts from each step plus total wall-clock duration
+ *
+ * @example
+ * ```ts
+ * const result = await runBrainMaintenance('/my/project', {
+ *   onProgress: (step, current, total) => {
+ *     console.log(`[${step}] ${current}/${total}`);
+ *   },
+ * });
+ * console.log(`Done in ${result.duration}ms`);
+ * ```
+ *
+ * @task T143
+ * @epic T134
+ */
+export async function runBrainMaintenance(projectRoot, options) {
+    const { skipDecay = false, skipConsolidation = false, skipReconciliation = false, skipEmbeddings = false, onProgress, } = options ?? {};
+    const startTime = Date.now();
+    // Default zero values for each step (used when step is skipped).
+    const decayResult = { affected: 0 };
+    const consolidationResult = { merged: 0, removed: 0 };
+    const reconciliationResult = {
+        decisionsFixed: 0,
+        observationsFixed: 0,
+        linksRemoved: 0,
+    };
+    const embeddingsResult = {
+        processed: 0,
+        skipped: 0,
+        errors: 0,
+    };
+    // Step 1: Temporal decay
+    if (!skipDecay) {
+        onProgress?.('decay', 0, 1);
+        const raw = await applyTemporalDecay(projectRoot);
+        decayResult.affected = raw.updated;
+        onProgress?.('decay', 1, 1);
+    }
+    // Step 2: Memory consolidation
+    if (!skipConsolidation) {
+        onProgress?.('consolidation', 0, 1);
+        const raw = await consolidateMemories(projectRoot);
+        consolidationResult.merged = raw.merged;
+        consolidationResult.removed = raw.archived;
+        onProgress?.('consolidation', 1, 1);
+    }
+    // Step 3: Cross-DB orphaned reference reconciliation
+    if (!skipReconciliation) {
+        onProgress?.('reconciliation', 0, 1);
+        const raw = await reconcileOrphanedRefs(projectRoot);
+        reconciliationResult.decisionsFixed = raw.decisionsFixed;
+        reconciliationResult.observationsFixed = raw.observationsFixed;
+        reconciliationResult.linksRemoved = raw.linksRemoved;
+        onProgress?.('reconciliation', 1, 1);
+    }
+    // Step 4: Embedding backfill (with per-item progress relay)
+    if (!skipEmbeddings) {
+        const raw = await populateEmbeddings(projectRoot, {
+            onProgress: (current, total) => {
+                onProgress?.('embeddings', current, total);
+            },
+        });
+        embeddingsResult.processed = raw.processed;
+        embeddingsResult.skipped = raw.skipped;
+        embeddingsResult.errors = raw.errors;
+    }
+    return {
+        decay: decayResult,
+        consolidation: consolidationResult,
+        reconciliation: reconciliationResult,
+        embeddings: embeddingsResult,
+        duration: Date.now() - startTime,
+    };
+}
+//# sourceMappingURL=brain-maintenance.js.map

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