@cleocode/core 2026.4.57 → 2026.4.59

package/dist/store/brain-sqlite.js

@@ -0,0 +1,320 @@
+/**
+ * SQLite store for brain.db via drizzle-orm/node-sqlite + node:sqlite (DatabaseSync).
+ *
+ * Separate database from tasks.db for cognitive infrastructure (decisions,
+ * patterns, learnings). Follows the same singleton + WAL + migration pattern
+ * as sqlite.ts.
+ *
+ * @epic T5149
+ * @task T5128
+ */
+import { mkdirSync } from 'node:fs';
+import { createRequire } from 'node:module';
+import { dirname, join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { drizzle } from 'drizzle-orm/node-sqlite';
+import { getCleoDirAbsolute } from '../paths.js';
+import * as brainSchema from './brain-schema.js';
+import { createSafetyBackup, ensureColumns, migrateWithRetry, reconcileJournal, tableExists, } from './migration-manager.js';
+import { openNativeDatabase } from './sqlite.js';
+const _require = createRequire(import.meta.url);
+/** Database file name within .cleo/ directory. */
+const DB_FILENAME = 'brain.db';
+/** Schema version for newly created brain databases. Single source of truth. */
+export const BRAIN_SCHEMA_VERSION = '1.0.0';
+/** Singleton state for lazy initialization. */
+let _db = null;
+let _nativeDb = null;
+let _dbPath = null;
+/** Guard against concurrent initialization (async migration). */
+let _initPromise = null;
+/** Whether sqlite-vec extension loaded successfully. */
+let _vecLoaded = false;
+/**
+ * Get the path to the brain.db SQLite database file.
+ */
+export function getBrainDbPath(cwd) {
+    return join(getCleoDirAbsolute(cwd), DB_FILENAME);
+}
+/**
+ * Resolve the path to the drizzle-brain migrations folder.
+ * Works from both src/ (dev via tsx) and dist/ (compiled via esbuild bundle).
+ *
+ * - Source layout: __dirname = src/store/ → need ../../migrations/drizzle-brain
+ * - Bundled layout: __dirname = dist/     → need ../migrations/drizzle-brain
+ */
+export function resolveBrainMigrationsFolder() {
+    const __filename = fileURLToPath(import.meta.url);
+    const __dirname = dirname(__filename);
+    const isBundled = __dirname.endsWith('/dist') || __dirname.endsWith('\\dist');
+    const pkgRoot = isBundled ? join(__dirname, '..') : join(__dirname, '..', '..');
+    return join(pkgRoot, 'migrations', 'drizzle-brain');
+}
+// tableExists — delegated to migration-manager.ts (T132)
+/**
+ * Run drizzle migrations to create/update brain.db tables.
+ *
+ * Delegates to shared migration-manager.ts for journal reconciliation,
+ * retry logic, and safety backups. See T132 for consolidation rationale.
+ *
+ * @task T5128
+ * @task T132 - Unified migration system
+ */
+function runBrainMigrations(nativeDb, db) {
+    const migrationsFolder = resolveBrainMigrationsFolder();
+    // Safety backup before any migration work
+    if (tableExists(nativeDb, 'brain_decisions') && _dbPath) {
+        createSafetyBackup(_dbPath);
+    }
+    // Bootstrap baseline + reconcile stale journal entries
+    reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
+    // Run pending migrations with SQLITE_BUSY retry.
+    // Pass nativeDb + existenceTable so migrateWithRetry can auto-reconcile any
+    // partial migration (Scenario 3) that slips through the proactive check above.
+    migrateWithRetry(db, migrationsFolder, nativeDb, 'brain_decisions', 'brain');
+    // Safety net: ensure all columns from T528/T531/T549 exist even if the
+    // migration files were never committed to git or the journal was not updated.
+    // ensureColumns uses PRAGMA table_info + ALTER TABLE ADD COLUMN — idempotent.
+    // T528: graph schema expansion — quality scoring, content hashing, last-activity.
+    // Note: last_activity_at uses nullable text (no non-constant default) because
+    // ALTER TABLE ADD COLUMN with datetime('now') default fails on non-empty tables.
+    ensureColumns(nativeDb, 'brain_page_nodes', [
+        { name: 'quality_score', ddl: 'real DEFAULT 0.5' },
+        { name: 'content_hash', ddl: 'text' },
+        { name: 'last_activity_at', ddl: 'text' },
+        { name: 'updated_at', ddl: 'text' },
+    ], 'brain');
+    // T531: quality score on typed brain tables
+    for (const table of [
+        'brain_decisions',
+        'brain_patterns',
+        'brain_learnings',
+        'brain_observations',
+    ]) {
+        ensureColumns(nativeDb, table, [{ name: 'quality_score', ddl: 'real' }], 'brain');
+    }
+    // T549: tiered + typed memory architecture
+    for (const table of [
+        'brain_decisions',
+        'brain_patterns',
+        'brain_learnings',
+        'brain_observations',
+    ]) {
+        ensureColumns(nativeDb, table, [
+            { name: 'memory_tier', ddl: "text DEFAULT 'short'" },
+            { name: 'memory_type', ddl: "text DEFAULT 'episodic'" },
+            { name: 'verified', ddl: 'integer NOT NULL DEFAULT 0' },
+            // valid_at uses nullable text (no datetime('now') default) because
+            // ALTER TABLE ADD COLUMN with non-constant defaults fails on non-empty tables.
+            { name: 'valid_at', ddl: 'text' },
+            { name: 'invalid_at', ddl: 'text' },
+            { name: 'source_confidence', ddl: "text DEFAULT 'agent'" },
+            { name: 'citation_count', ddl: 'integer NOT NULL DEFAULT 0' },
+        ], 'brain');
+    }
+    // T632 root-cause fix: the migration journal reconciler (Sub-case B) now uses
+    // a per-migration DDL probe instead of wholesale-marking-all-applied. ALTER TABLE
+    // ADD COLUMN migrations (T417 agent, T528 provenance) now run correctly when
+    // their columns are missing.
+    //
+    // The previous `ensureColumns` band-aids (for `agent` and `provenance`) were
+    // removed in v2026.4.54 alongside the reconciler fix. If schema regressions
+    // recur, the right action is to debug `probeAndMarkApplied` in
+    // migration-manager.ts — NOT to add new band-aids here.
+    // T626-M1: Normalize co_retrieved edge type — idempotent safety-net UPDATE.
+    // The shipped Hebbian strengthener emitted edge_type = 'relates_to' instead of
+    // 'co_retrieved'. Relabel only rows from the consolidation provenance so no
+    // semantic edges are affected. The Drizzle migration file does the same UPDATE;
+    // this guard handles installs where the journal reconciler already marked
+    // the migration applied before the SQL ran.
+    if (tableExists(nativeDb, 'brain_page_edges')) {
+        nativeDb
+            .prepare(`UPDATE brain_page_edges
+         SET edge_type = 'co_retrieved'
+         WHERE edge_type = 'relates_to'
+           AND provenance LIKE 'consolidation:%'`)
+            .run();
+    }
+}
+/**
+ * Load the sqlite-vec extension into a native DatabaseSync instance.
+ * Returns true if the extension loaded successfully, false otherwise.
+ *
+ * The extension enables vec0 virtual tables for vector similarity search.
+ * Requires the database to be opened with allowExtension: true.
+ *
+ * @task T5157
+ */
+function loadBrainVecExtension(nativeDb) {
+    try {
+        const sqliteVec = _require('sqlite-vec');
+        sqliteVec.load(nativeDb);
+        return true;
+    }
+    catch {
+        // sqlite-vec not available or failed to load — non-fatal
+        return false;
+    }
+}
+/**
+ * Create the vec0 virtual table for brain embeddings.
+ * Called after migrations complete and sqlite-vec extension is loaded.
+ *
+ * The vec0 table is not managed by Drizzle (virtual tables are not
+ * supported by drizzle-orm's SQLite schema). Created via raw SQL.
+ *
+ * @task T5157
+ */
+function initializeBrainVec(nativeDb) {
+    nativeDb
+        .prepare('CREATE VIRTUAL TABLE IF NOT EXISTS brain_embeddings USING vec0(id TEXT PRIMARY KEY, embedding FLOAT[384])')
+        .run();
+}
+/**
+ * Check whether the sqlite-vec extension is loaded for the current brain.db.
+ */
+export function isBrainVecLoaded() {
+    return _vecLoaded;
+}
+/**
+ * Initialize the default embedding provider when brain.embedding.enabled is true.
+ *
+ * Called asynchronously after getBrainDb() completes its synchronous setup.
+ * Uses dynamic import to avoid circular dependencies and keep the heavy
+ * @huggingface/transformers bundle out of the critical startup path.
+ *
+ * Best-effort: errors are swallowed by the caller so DB access is never blocked.
+ *
+ * @task T539
+ */
+async function initEmbeddingProvider(cwd) {
+    try {
+        const { loadConfig } = await import('../config.js');
+        const config = await loadConfig(cwd);
+        if (config.brain?.embedding?.enabled) {
+            const { initDefaultProvider } = await import('../memory/brain-embedding.js');
+            await initDefaultProvider();
+        }
+    }
+    catch {
+        // Config load or provider init failed — non-fatal, embedding stays unavailable
+    }
+}
+/**
+ * Initialize the brain.db SQLite database (lazy, singleton).
+ * Creates the database file and tables if they don't exist.
+ * Returns the drizzle ORM instance (async via sqlite-proxy).
+ *
+ * Uses a promise guard so concurrent callers wait for the same
+ * initialization to complete (migrations are async).
+ */
+export async function getBrainDb(cwd) {
+    const requestedPath = getBrainDbPath(cwd);
+    // If singleton exists but points to different path, reset it
+    if (_db && _dbPath !== requestedPath) {
+        resetBrainDbState();
+    }
+    if (_db)
+        return _db;
+    // If already initializing, wait for the in-flight init
+    if (_initPromise)
+        return _initPromise;
+    _initPromise = (async () => {
+        const dbPath = requestedPath;
+        _dbPath = dbPath;
+        // Ensure directory exists
+        mkdirSync(dirname(dbPath), { recursive: true });
+        // Open file-backed SQLite via node:sqlite with WAL mode.
+        // allowExtension: true enables sqlite-vec extension loading.
+        const nativeDb = openNativeDatabase(dbPath, { allowExtension: true });
+        _nativeDb = nativeDb;
+        // Load sqlite-vec extension for vector similarity search (T5157).
+        // Non-fatal if unavailable — vec0 tables simply won't be created.
+        _vecLoaded = loadBrainVecExtension(nativeDb);
+        // Create drizzle ORM wrapper via node-sqlite
+        const db = drizzle({ client: nativeDb, schema: brainSchema });
+        // Run drizzle migrations (creates/updates tables)
+        runBrainMigrations(nativeDb, db);
+        // Create vec0 virtual table for embeddings if extension is loaded (T5157).
+        // Must run after migrations so the schema is consistent.
+        if (_vecLoaded) {
+            initializeBrainVec(nativeDb);
+        }
+        // Seed schema version for new databases (no-op if already set)
+        nativeDb
+            .prepare(`INSERT OR IGNORE INTO brain_schema_meta (key, value) VALUES ('schemaVersion', '${BRAIN_SCHEMA_VERSION}')`)
+            .run();
+        // Set singleton only after migrations complete
+        _db = db;
+        // Wire the default embedding provider when vec is loaded and embedding is enabled.
+        // Best-effort, async, never blocks DB access. (T539)
+        if (_vecLoaded) {
+            setImmediate(() => {
+                initEmbeddingProvider(cwd).catch(() => {
+                    // Non-fatal — embedding will be unavailable until next startup
+                });
+            });
+        }
+        return db;
+    })();
+    try {
+        return await _initPromise;
+    }
+    finally {
+        _initPromise = null;
+    }
+}
+/**
+ * Close the brain.db database connection and release resources.
+ */
+export function closeBrainDb() {
+    if (_nativeDb) {
+        try {
+            if (_nativeDb.isOpen) {
+                _nativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nativeDb = null;
+    }
+    _db = null;
+    _dbPath = null;
+    _vecLoaded = false;
+}
+/**
+ * Reset brain.db singleton state without saving.
+ * Used during tests or when database file is recreated.
+ * Safe to call multiple times.
+ */
+export function resetBrainDbState() {
+    if (_nativeDb) {
+        try {
+            if (_nativeDb.isOpen) {
+                _nativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nativeDb = null;
+    }
+    _db = null;
+    _dbPath = null;
+    _initPromise = null;
+    _vecLoaded = false;
+}
+/**
+ * Get the underlying node:sqlite DatabaseSync instance for brain.db.
+ * Useful for direct PRAGMA calls or raw SQL operations.
+ * Returns null if the database hasn't been initialized.
+ */
+export function getBrainNativeDb() {
+    return _nativeDb;
+}
+/**
+ * Re-export brain schema for external use.
+ */
+export { brainSchema };
+//# sourceMappingURL=brain-sqlite.js.map

package/dist/store/brain-sqlite.js.map

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package/dist/store/cache.js

@@ -0,0 +1,168 @@
+/**
+ * Index caching for O(1) label/phase/hierarchy lookups.
+ * Ported from lib/data/cache.sh
+ *
+ * @epic T4454
+ * @task T4530
+ */
+/**
+ * In-memory cache for task indices with checksum-based staleness detection.
+ */
+export class TaskCache {
+    labelIndex = new Map();
+    phaseIndex = new Map();
+    parentIndex = new Map();
+    childrenIndex = new Map();
+    depthIndex = new Map();
+    checksum = '';
+    initialized = false;
+    /**
+     * Compute a checksum from task data for staleness detection.
+     */
+    computeChecksum(tasks) {
+        return tasks
+            .map((t) => `${t.id}:${t.status}:${t.parentId ?? ''}:${t.phase ?? ''}:${(t.labels ?? []).join(',')}`)
+            .sort()
+            .join('|');
+    }
+    /**
+     * Initialize or rebuild cache from tasks.
+     * Returns true if cache was rebuilt, false if already valid.
+     */
+    init(tasks) {
+        const newChecksum = this.computeChecksum(tasks);
+        if (this.initialized && newChecksum === this.checksum) {
+            return false;
+        }
+        this.buildLabelIndex(tasks);
+        this.buildPhaseIndex(tasks);
+        this.buildHierarchyIndex(tasks);
+        this.checksum = newChecksum;
+        this.initialized = true;
+        return true;
+    }
+    buildLabelIndex(tasks) {
+        this.labelIndex.clear();
+        for (const task of tasks) {
+            if (!task.labels?.length)
+                continue;
+            for (const label of task.labels) {
+                const existing = this.labelIndex.get(label) ?? [];
+                existing.push(task.id);
+                this.labelIndex.set(label, existing);
+            }
+        }
+    }
+    buildPhaseIndex(tasks) {
+        this.phaseIndex.clear();
+        for (const task of tasks) {
+            if (!task.phase)
+                continue;
+            const existing = this.phaseIndex.get(task.phase) ?? [];
+            existing.push(task.id);
+            this.phaseIndex.set(task.phase, existing);
+        }
+    }
+    buildHierarchyIndex(tasks) {
+        this.parentIndex.clear();
+        this.childrenIndex.clear();
+        this.depthIndex.clear();
+        const taskMap = new Map(tasks.map((t) => [t.id, t]));
+        for (const task of tasks) {
+            this.parentIndex.set(task.id, task.parentId ?? null);
+            if (task.parentId) {
+                const siblings = this.childrenIndex.get(task.parentId) ?? [];
+                siblings.push(task.id);
+                this.childrenIndex.set(task.parentId, siblings);
+            }
+        }
+        // Compute depths
+        for (const task of tasks) {
+            let depth = 0;
+            let current = task;
+            const visited = new Set();
+            while (current.parentId && !visited.has(current.parentId)) {
+                visited.add(current.parentId);
+                const parent = taskMap.get(current.parentId);
+                if (!parent)
+                    break;
+                depth++;
+                current = parent;
+            }
+            this.depthIndex.set(task.id, depth);
+        }
+    }
+    /** Get task IDs by label. */
+    getTasksByLabel(label) {
+        return this.labelIndex.get(label) ?? [];
+    }
+    /** Get task IDs by phase. */
+    getTasksByPhase(phase) {
+        return this.phaseIndex.get(phase) ?? [];
+    }
+    /** Get all labels. */
+    getAllLabels() {
+        return [...this.labelIndex.keys()];
+    }
+    /** Get all phases. */
+    getAllPhases() {
+        return [...this.phaseIndex.keys()];
+    }
+    /** Get label count for a specific label. */
+    getLabelCount(label) {
+        return this.getTasksByLabel(label).length;
+    }
+    /** Get parent ID for a task. */
+    getParent(taskId) {
+        return this.parentIndex.get(taskId) ?? null;
+    }
+    /** Get children IDs for a task. */
+    getChildren(taskId) {
+        return this.childrenIndex.get(taskId) ?? [];
+    }
+    /** Get depth for a task. */
+    getDepth(taskId) {
+        return this.depthIndex.get(taskId) ?? 0;
+    }
+    /** Get child count. */
+    getChildCount(taskId) {
+        return this.getChildren(taskId).length;
+    }
+    /** Get root tasks (no parent). */
+    getRootTasks() {
+        return [...this.parentIndex.entries()]
+            .filter(([, parent]) => parent === null)
+            .map(([id]) => id);
+    }
+    /** Get leaf tasks (no children). */
+    getLeafTasks() {
+        const parentSet = new Set(this.childrenIndex.keys());
+        return [...this.parentIndex.keys()].filter((id) => !parentSet.has(id) || this.getChildCount(id) === 0);
+    }
+    /** Force invalidation and rebuild. */
+    invalidate() {
+        this.labelIndex.clear();
+        this.phaseIndex.clear();
+        this.parentIndex.clear();
+        this.childrenIndex.clear();
+        this.depthIndex.clear();
+        this.checksum = '';
+        this.initialized = false;
+    }
+    /** Get cache statistics. */
+    getStats() {
+        let maxDepth = 0;
+        for (const d of this.depthIndex.values()) {
+            if (d > maxDepth)
+                maxDepth = d;
+        }
+        return {
+            initialized: this.initialized,
+            labelCount: this.labelIndex.size,
+            phaseCount: this.phaseIndex.size,
+            taskCount: this.parentIndex.size,
+            maxDepth,
+        };
+    }
+}
+//# sourceMappingURL=cache.js.map

package/dist/store/cache.js.map

@@ -0,0 +1 @@
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package/dist/store/chain-schema.js

@@ -0,0 +1,51 @@
+/**
+ * Drizzle ORM schema for WarpChain storage in tasks.db.
+ *
+ * Tables: warp_chains, warp_chain_instances
+ * Stores chain definitions and runtime instances bound to epics.
+ *
+ * @task T5403
+ */
+import { sql } from 'drizzle-orm';
+import { index, integer, sqliteTable, text } from 'drizzle-orm/sqlite-core';
+/** Chain instance status values. */
+export const WARP_CHAIN_INSTANCE_STATUSES = [
+    'pending',
+    'active',
+    'completed',
+    'failed',
+    'cancelled',
+];
+// === WARP_CHAINS TABLE ===
+/** Stored WarpChain definitions (serialized as JSON). */
+export const warpChains = sqliteTable('warp_chains', {
+    id: text('id').primaryKey(),
+    name: text('name').notNull(),
+    version: text('version').notNull(),
+    description: text('description'),
+    definition: text('definition').notNull(), // JSON-serialized WarpChain
+    validated: integer('validated', { mode: 'boolean' }).default(false),
+    createdAt: text('created_at').default(sql `(datetime('now'))`),
+    updatedAt: text('updated_at').default(sql `(datetime('now'))`),
+}, (table) => [index('idx_warp_chains_name').on(table.name)]);
+// === WARP_CHAIN_INSTANCES TABLE ===
+/** Runtime chain instances bound to epics. */
+export const warpChainInstances = sqliteTable('warp_chain_instances', {
+    id: text('id').primaryKey(),
+    chainId: text('chain_id')
+        .notNull()
+        .references(() => warpChains.id, { onDelete: 'cascade' }),
+    epicId: text('epic_id').notNull(),
+    variables: text('variables'), // JSON
+    stageToTask: text('stage_to_task'), // JSON
+    status: text('status').notNull().default('pending'),
+    currentStage: text('current_stage'),
+    gateResults: text('gate_results'), // JSON array of GateResult
+    createdAt: text('created_at').default(sql `(datetime('now'))`),
+    updatedAt: text('updated_at').default(sql `(datetime('now'))`),
+}, (table) => [
+    index('idx_warp_instances_chain').on(table.chainId),
+    index('idx_warp_instances_epic').on(table.epicId),
+    index('idx_warp_instances_status').on(table.status),
+]);
+//# sourceMappingURL=chain-schema.js.map

package/dist/store/chain-schema.js.map

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