@cleocode/core 2026.4.13 → 2026.4.14

package/dist/store/brain-sqlite.js

@@ -1,222 +0,0 @@
-/**
- * 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, 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
-    migrateWithRetry(db, migrationsFolder);
-}
-/**
- * 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 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;
-        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

@@ -1,168 +0,0 @@
-/**
- * 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

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

@@ -1,51 +0,0 @@
-/**
- * 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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package/dist/store/cleanup-legacy.js

@@ -1,171 +0,0 @@
-/**
- * Idempotent cleanup of legacy and stray CLEO database files.
- *
- * Provides two independent cleanup functions:
- *
- * 1. {@link detectAndRemoveLegacyGlobalFiles} — removes stale files left at
- *    the global CLEO home directory (`getCleoHome()`) by pre-v2026.4.11
- *    naming migrations. Safe to call on repeat invocations — existence-checks
- *    guard every deletion.
- *
- *    Files targeted (see ADR-036 §Decision/Global-Tier table):
- *      - workspace.db              (pre-nexus naming relic)
- *      - workspace.db.bak-pre-rename  (safety copy from a long-landed rename)
- *      - workspace.db-shm          (SQLite shared-memory sidecar of workspace.db)
- *      - workspace.db-shm-wal      (SQLite WAL sidecar of workspace.db)
- *      - nexus-pre-cleo.db.bak     (pre-CLEO backup of nexus — migration complete)
- *
- *    Live files (nexus.db, signaldock.db, machine-key, config.json, etc.) are
- *    NEVER touched. The function only acts on the explicit LEGACY_FILES list.
- *
- * 2. {@link detectAndRemoveStrayProjectNexus} — removes a stray
- *    `{projectRoot}/.cleo/nexus.db` that violates ADR-036's global-only
- *    nexus contract. Some pre-v2026.4.11 code path accidentally created a
- *    zero-byte nexus.db at project tier; this cleans it up on first run.
- *
- * @task T304
- * @task T307
- * @epic T299
- * @adr ADR-036
- * @why v2026.4.10 left workspace.db and pre-cleo backups at global tier;
- *   ADR-036 mandates their deletion to eliminate diagnostic confusion and
- *   false impressions of active legacy databases.
- */
-import fs from 'node:fs';
-import path from 'node:path';
-import { getLogger } from '../logger.js';
-import { getCleoHome } from '../paths.js';
-// ---------------------------------------------------------------------------
-// Constants
-// ---------------------------------------------------------------------------
-/**
- * Exhaustive list of legacy filenames that MUST be removed from the global
- * CLEO home directory. No other files are touched.
- *
- * @task T304
- */
-const LEGACY_FILES = [
-    'workspace.db',
-    'workspace.db.bak-pre-rename',
-    'workspace.db-shm',
-    'workspace.db-shm-wal',
-    'nexus-pre-cleo.db.bak',
-];
-// ---------------------------------------------------------------------------
-// Implementation
-// ---------------------------------------------------------------------------
-/**
- * Detect and remove legacy global-tier files from the CLEO home directory.
- *
- * Idempotent: safe to call when some or all files are already absent. Each
- * file is individually existence-checked before attempting deletion. Failures
- * on individual files are captured in `errors` rather than thrown, so the
- * caller receives a complete picture of what was (and was not) cleaned up.
- *
- * Logs each successful deletion at `info` level and each failure at `warn`
- * level via the shared pino logger.
- *
- * @param cleoHomeOverride - Optional directory override for tests. When
- *   omitted the canonical `getCleoHome()` path is used. Prefer passing this
- *   parameter in test harnesses rather than mutating `CLEO_HOME` environment
- *   variables, as it avoids global state contamination between test runs.
- * @returns A {@link LegacyCleanupResult} describing what was removed and any
- *   errors encountered.
- *
- * @example
- * ```typescript
- * // Production usage (runs against real global home)
- * const result = detectAndRemoveLegacyGlobalFiles();
- * if (result.removed.length > 0) {
- *   // Legacy files were cleaned up
- * }
- *
- * // Test usage (runs against tmp directory)
- * const result = detectAndRemoveLegacyGlobalFiles('/tmp/fake-cleo-home');
- * ```
- *
- * @task T304
- * @epic T299
- */
-export function detectAndRemoveLegacyGlobalFiles(cleoHomeOverride) {
-    const log = getLogger('cleanup-legacy');
-    const cleoHome = cleoHomeOverride ?? getCleoHome();
-    const removed = [];
-    const errors = [];
-    for (const fileName of LEGACY_FILES) {
-        const fullPath = path.join(cleoHome, fileName);
-        try {
-            if (fs.existsSync(fullPath)) {
-                fs.unlinkSync(fullPath);
-                removed.push(fileName);
-                log.info({ file: fullPath }, 'Removed legacy global file');
-            }
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            errors.push({ file: fileName, error: message });
-            log.warn({ file: fullPath, error: message }, 'Failed to remove legacy global file');
-        }
-    }
-    return { removed, errors };
-}
-/**
- * Detect and remove a stray project-tier `.cleo/nexus.db` file.
- *
- * ADR-036 declares nexus.db as **global-only** — it lives exclusively under
- * `getCleoHome()` (e.g. `~/.local/share/cleo/nexus.db` on Linux). A
- * zero-byte stray was discovered at `/mnt/projects/cleocode/.cleo/nexus.db`
- * (created 2026-03-31), likely produced by an early `cleo init` / `cleo
- * nexus init` invocation that ran before the canonical path was fully wired
- * through `getNexusDbPath()`.
- *
- * This function is idempotent: calling it when no stray file exists is a
- * no-op. It is designed to be called once per CLI startup (alongside
- * {@link detectAndRemoveLegacyGlobalFiles}) so that users who upgrade to
- * v2026.4.11 have the stray silently cleaned up on the first `cleo` run.
- *
- * @param projectRoot - Absolute path to the project root directory. When
- *   omitted the caller is responsible for supplying the current project
- *   root from `getProjectRoot()`. An override parameter is accepted here to
- *   keep tests hermetic (avoids reading live `process.cwd()` state).
- * @returns A {@link StrayNexusCleanupResult} indicating whether a file was
- *   removed and the absolute path that was checked.
- *
- * @example
- * ```typescript
- * // Production usage
- * import { getProjectRoot } from '../paths.js';
- * const result = detectAndRemoveStrayProjectNexus(getProjectRoot());
- * if (result.removed) {
- *   // Stray project-tier nexus.db has been cleaned up
- * }
- *
- * // Test usage (hermetic)
- * const result = detectAndRemoveStrayProjectNexus('/tmp/fake-project-root');
- * ```
- *
- * @task T307
- * @epic T299
- * @adr ADR-036
- * @why ADR-036 §Decision/Global-Tier: nexus.db is global-only. A stray
- *   project-tier copy was created by pre-v2026.4.11 code and must be removed
- *   to prevent diagnostic confusion and guard against future regressions.
- */
-export function detectAndRemoveStrayProjectNexus(projectRoot) {
-    const log = getLogger('cleanup-legacy');
-    const strayPath = path.join(projectRoot, '.cleo', 'nexus.db');
-    if (fs.existsSync(strayPath)) {
-        try {
-            fs.unlinkSync(strayPath);
-            log.warn({ path: strayPath }, 'Removed stray project-tier nexus.db (violates ADR-036 global-only contract)');
-            return { removed: true, path: strayPath };
-        }
-        catch (err) {
-            const message = err instanceof Error ? err.message : String(err);
-            log.warn({ path: strayPath, error: message }, 'Failed to remove stray project-tier nexus.db — manual deletion may be required');
-            return { removed: false, path: strayPath };
-        }
-    }
-    return { removed: false, path: strayPath };
-}
-//# sourceMappingURL=cleanup-legacy.js.map

package/dist/store/cleanup-legacy.js.map

@@ -1 +0,0 @@
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