@cleocode/core 2.0.0

package/dist/store/sqlite-data-accessor.js.map

@@ -0,0 +1 @@
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package/dist/store/sqlite.d.ts

@@ -0,0 +1,106 @@
+/**
+ * SQLite store via drizzle-orm/node-sqlite + node:sqlite (DatabaseSync).
+ *
+ * Zero native npm dependencies, 100% cross-platform (Windows/Linux/macOS).
+ * File-backed SQLite with WAL mode for multi-process concurrent access.
+ * Database stored at .cleo/tasks.db.
+ *
+ * Architecture: node:sqlite provides the synchronous file-backed SQLite engine,
+ * wrapped via drizzle-orm/node-sqlite for a fully synchronous interface. All
+ * writes go directly to disk through SQLite's native WAL mechanism -- no
+ * saveToFile() pattern needed.
+ *
+ * @epic T4454
+ * @task T4817 - node:sqlite engine migration (ADR-006, ADR-010)
+ * @task T4810 - Data loss prevention guards
+ */
+import type { DatabaseSync as _DatabaseSyncType } from 'node:sqlite';
+type DatabaseSync = _DatabaseSyncType;
+declare const DatabaseSync: new (path: import("fs").PathLike, options?: import("node:sqlite").DatabaseSyncOptions | undefined) => DatabaseSync;
+import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+import * as schema from './tasks-schema.js';
+/**
+ * Open a node:sqlite DatabaseSync with CLEO standard pragmas.
+ *
+ * CRITICAL: WAL mode is verified, not just requested. If another process holds
+ * an EXCLUSIVE lock in DELETE mode, PRAGMA journal_mode=WAL silently returns
+ * 'delete'. This caused data loss (T5173) when concurrent MCP servers opened
+ * the same database — writes were silently dropped under lock contention.
+ */
+export declare function openNativeDatabase(path: string, options?: {
+    readonly?: boolean;
+    timeout?: number;
+    enableWal?: boolean;
+    allowExtension?: boolean;
+}): DatabaseSync;
+/** Schema version for newly created databases. Single source of truth. */
+export declare const SQLITE_SCHEMA_VERSION = "2.0.0";
+/**
+ * Get the path to the SQLite database file.
+ */
+export declare function getDbPath(cwd?: string): string;
+/**
+ * Initialize the SQLite database (lazy, singleton).
+ * Creates the database file and tables if they don't exist.
+ * Returns the drizzle ORM instance (node-sqlite driver).
+ *
+ * Uses a promise guard so concurrent callers wait for the same
+ * initialization to complete (migrations are async).
+ */
+export declare function getDb(cwd?: string): Promise<NodeSQLiteDatabase<typeof schema>>;
+/**
+ * Resolve the path to the drizzle migrations folder.
+ * Works from both src/ (dev via tsx) and dist/ (compiled).
+ */
+export declare function resolveMigrationsFolder(): string;
+/**
+ * Check if an error is a SQLite BUSY error (database locked by another process).
+ * node:sqlite throws native Error with message containing the SQLite error code.
+ * @task T5185
+ */
+export declare function isSqliteBusy(err: unknown): boolean;
+/**
+ * Close the database connection and release resources.
+ */
+export declare function closeDb(): void;
+/**
+ * Reset database singleton state without saving.
+ * Used during migrations when database file is deleted and recreated.
+ * Safe to call multiple times.
+ */
+export declare function resetDbState(): void;
+/**
+ * Get the schema version from the database.
+ */
+export declare function getSchemaVersion(cwd?: string): Promise<string | null>;
+/**
+ * Check if the database file exists.
+ */
+export declare function dbExists(cwd?: string): boolean;
+/**
+ * Get the underlying node:sqlite DatabaseSync instance.
+ * Useful for direct PRAGMA calls or raw SQL operations.
+ * Returns null if the database hasn't been initialized.
+ */
+export declare function getNativeDb(): DatabaseSync | null;
+/**
+ * Get the underlying node:sqlite DatabaseSync instance for tasks.db.
+ * Alias for getNativeDb() — mirrors getBrainNativeDb() naming convention.
+ */
+export declare function getNativeTasksDb(): DatabaseSync | null;
+/**
+ * Re-export schema for external use.
+ */
+export { schema };
+export type { NodeSQLiteDatabase };
+/**
+ * Close ALL database singletons (tasks.db, brain.db, nexus.db).
+ *
+ * Must be called before deleting temp directories on Windows, where
+ * SQLite holds exclusive file handles on .db, .db-wal, and .db-shm files.
+ * Safe to call even if some databases were never opened.
+ *
+ * @task T5508
+ */
+export declare function closeAllDatabases(): Promise<void>;
+//# sourceMappingURL=sqlite.d.ts.map

package/dist/store/sqlite.d.ts.map

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package/dist/store/sqlite.js

@@ -0,0 +1,481 @@
+/**
+ * SQLite store via drizzle-orm/node-sqlite + node:sqlite (DatabaseSync).
+ *
+ * Zero native npm dependencies, 100% cross-platform (Windows/Linux/macOS).
+ * File-backed SQLite with WAL mode for multi-process concurrent access.
+ * Database stored at .cleo/tasks.db.
+ *
+ * Architecture: node:sqlite provides the synchronous file-backed SQLite engine,
+ * wrapped via drizzle-orm/node-sqlite for a fully synchronous interface. All
+ * writes go directly to disk through SQLite's native WAL mechanism -- no
+ * saveToFile() pattern needed.
+ *
+ * @epic T4454
+ * @task T4817 - node:sqlite engine migration (ADR-006, ADR-010)
+ * @task T4810 - Data loss prevention guards
+ */
+import { copyFileSync, existsSync, mkdirSync, renameSync, unlinkSync } from 'node:fs';
+import { createRequire } from 'node:module';
+const _require = createRequire(import.meta.url);
+const { DatabaseSync } = _require('node:sqlite');
+import { dirname, join, resolve, sep } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { eq } from 'drizzle-orm';
+import { readMigrationFiles } from 'drizzle-orm/migrator';
+import { drizzle } from 'drizzle-orm/node-sqlite';
+import { migrate } from 'drizzle-orm/node-sqlite/migrator';
+import { getLogger } from '../logger.js';
+import { getCleoDirAbsolute } from '../paths.js';
+import { listSqliteBackups } from './sqlite-backup.js';
+import * as schema from './tasks-schema.js';
+/**
+ * Open a node:sqlite DatabaseSync with CLEO standard pragmas.
+ *
+ * CRITICAL: WAL mode is verified, not just requested. If another process holds
+ * an EXCLUSIVE lock in DELETE mode, PRAGMA journal_mode=WAL silently returns
+ * 'delete'. This caused data loss (T5173) when concurrent MCP servers opened
+ * the same database — writes were silently dropped under lock contention.
+ */
+export function openNativeDatabase(path, options) {
+    const db = new DatabaseSync(path, {
+        enableForeignKeyConstraints: true,
+        readOnly: options?.readonly ?? false,
+        timeout: options?.timeout ?? 5000,
+        allowExtension: options?.allowExtension ?? false,
+    });
+    // Set busy_timeout FIRST so WAL pragma can wait for locks
+    db.exec('PRAGMA busy_timeout=5000');
+    // Enable WAL for concurrent multi-process access (ADR-006, ADR-010)
+    if (options?.enableWal !== false) {
+        const MAX_WAL_RETRIES = 3;
+        const RETRY_DELAY_MS = 200;
+        let walSet = false;
+        for (let attempt = 1; attempt <= MAX_WAL_RETRIES; attempt++) {
+            db.exec('PRAGMA journal_mode=WAL');
+            // CRITICAL: Verify WAL was actually set — the PRAGMA returns the mode
+            // that was applied, which may be 'delete' if another connection holds a lock
+            const result = db.prepare('PRAGMA journal_mode').get();
+            const currentMode = result?.journal_mode?.toLowerCase?.() ?? 'unknown';
+            if (currentMode === 'wal') {
+                walSet = true;
+                break;
+            }
+            // WAL not set — another connection likely holds an EXCLUSIVE lock
+            if (attempt < MAX_WAL_RETRIES) {
+                // Sync sleep via Atomics for retry delay (node:sqlite is sync-only)
+                const buf = new SharedArrayBuffer(4);
+                Atomics.wait(new Int32Array(buf), 0, 0, RETRY_DELAY_MS * attempt);
+            }
+        }
+        if (!walSet) {
+            // Verify one final time
+            const finalResult = db.prepare('PRAGMA journal_mode').get();
+            const finalMode = finalResult?.journal_mode?.toLowerCase?.() ?? 'unknown';
+            if (finalMode !== 'wal') {
+                db.close();
+                throw new Error(`CRITICAL: Failed to set WAL journal mode after ${MAX_WAL_RETRIES} attempts. ` +
+                    `Database is in '${finalMode}' mode. Another process likely holds an EXCLUSIVE lock ` +
+                    `on ${path}. Refusing to open — concurrent writes in DELETE mode cause data loss. ` +
+                    `Kill other cleo/MCP processes and retry. (T5173)`);
+            }
+        }
+    }
+    // Standard CLEO pragmas
+    db.exec('PRAGMA foreign_keys=ON');
+    return db;
+}
+/** Database file name within .cleo/ directory. */
+const DB_FILENAME = 'tasks.db';
+/** Schema version for newly created databases. Single source of truth. */
+export const SQLITE_SCHEMA_VERSION = '2.0.0';
+const SCHEMA_VERSION = SQLITE_SCHEMA_VERSION;
+/** Singleton state for lazy initialization. */
+let _db = null;
+let _nativeDb = null;
+let _dbPath = null;
+/** Guard against concurrent initialization (async migration). */
+let _initPromise = null;
+/** Guard: git-tracking check runs only once per process. */
+let _gitTrackingChecked = false;
+/**
+ * Get the path to the SQLite database file.
+ */
+export function getDbPath(cwd) {
+    return join(getCleoDirAbsolute(cwd), DB_FILENAME);
+}
+/**
+ * Minimum task count in a backup to consider it a valid recovery source.
+ * Prevents restoring from a backup that's also empty or nearly empty.
+ * @task T5188
+ */
+const MIN_BACKUP_TASK_COUNT = 10;
+/**
+ * Auto-recover from backup if the database has tables but zero tasks
+ * and a backup with data exists.
+ *
+ * Root cause (T5188): WAL/SHM files were tracked by git. On branch switch,
+ * git overwrites the WAL with an empty (committed) version, discarding all
+ * pending WAL writes. The main DB file (which may not have been checkpointed)
+ * appears empty because all recent writes were in the WAL.
+ *
+ * This function runs after migrations (so tables exist) and before the
+ * singleton is set. It checks if the tasks table is empty and a VACUUM INTO
+ * backup exists with real data. If so, it closes the current connection,
+ * replaces the DB file from backup, and re-opens.
+ *
+ * @task T5188
+ */
+async function autoRecoverFromBackup(nativeDb, dbPath, cwd) {
+    const log = getLogger('sqlite');
+    try {
+        // Count tasks in current database
+        const countResult = nativeDb.prepare('SELECT COUNT(*) as cnt FROM tasks').get();
+        const taskCount = countResult?.cnt ?? 0;
+        if (taskCount > 0)
+            return; // Database has data, no recovery needed
+        // Database is empty — check for backups
+        const backups = listSqliteBackups(cwd);
+        if (backups.length === 0) {
+            // No backups available — this is a genuinely new database
+            return;
+        }
+        // Check the newest backup for task count
+        const newestBackup = backups[0];
+        // Open backup read-only to verify it has data
+        const backupDb = new DatabaseSync(newestBackup.path, { readOnly: true });
+        let backupTaskCount = 0;
+        try {
+            const backupCount = backupDb.prepare('SELECT COUNT(*) as cnt FROM tasks').get();
+            backupTaskCount = backupCount?.cnt ?? 0;
+        }
+        finally {
+            backupDb.close();
+        }
+        if (backupTaskCount < MIN_BACKUP_TASK_COUNT) {
+            // Backup also has very few tasks — not a reliable recovery source
+            return;
+        }
+        // We have an empty database AND a backup with data — auto-recover
+        log.warn({ dbPath, backupPath: newestBackup.path, backupTasks: backupTaskCount }, `Empty database detected with ${backupTaskCount}-task backup available. ` +
+            'Auto-recovering from backup. This likely happened because git-tracked ' +
+            'WAL/SHM files were overwritten during a branch switch (T5188).');
+        // Close current connection
+        nativeDb.close();
+        // Remove stale WAL/SHM files that may have been corrupted by git
+        const walPath = dbPath + '-wal';
+        const shmPath = dbPath + '-shm';
+        try {
+            unlinkSync(walPath);
+        }
+        catch {
+            /* may not exist */
+        }
+        try {
+            unlinkSync(shmPath);
+        }
+        catch {
+            /* may not exist */
+        }
+        // Restore from backup (atomic: copy to temp, rename)
+        const tempPath = dbPath + '.recovery-tmp';
+        copyFileSync(newestBackup.path, tempPath);
+        // Rename in place — on the same filesystem this is atomic
+        renameSync(tempPath, dbPath);
+        log.info({ dbPath, backupPath: newestBackup.path, restoredTasks: backupTaskCount }, 'Database auto-recovered from backup successfully.');
+        // Re-open the restored database — update the native singleton
+        const restoredNativeDb = openNativeDatabase(dbPath);
+        _nativeDb = restoredNativeDb;
+        // Re-run migrations on restored DB to ensure schema is current
+        const restoredDb = drizzle({ client: restoredNativeDb, schema });
+        runMigrations(restoredNativeDb, restoredDb);
+        // Update the singleton drizzle instance
+        _db = restoredDb;
+    }
+    catch (err) {
+        // Auto-recovery failure is non-fatal — log and continue with empty DB
+        log.error({ err, dbPath }, 'Auto-recovery from backup failed. Continuing with empty database.');
+    }
+}
+/**
+ * Initialize the SQLite database (lazy, singleton).
+ * Creates the database file and tables if they don't exist.
+ * Returns the drizzle ORM instance (node-sqlite driver).
+ *
+ * Uses a promise guard so concurrent callers wait for the same
+ * initialization to complete (migrations are async).
+ */
+export async function getDb(cwd) {
+    const requestedPath = getDbPath(cwd);
+    // If singleton exists but points to different path, reset it
+    if (_db && _dbPath !== requestedPath) {
+        resetDbState();
+    }
+    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
+        const nativeDb = openNativeDatabase(dbPath);
+        _nativeDb = nativeDb;
+        // Create drizzle ORM wrapper via node-sqlite
+        const db = drizzle({ client: nativeDb, schema });
+        // Run drizzle migrations (creates/updates tables)
+        runMigrations(nativeDb, db);
+        // Seed schema version for new databases (no-op if already set)
+        nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('schemaVersion', '${SCHEMA_VERSION}')`);
+        nativeDb.exec(`INSERT OR IGNORE INTO schema_meta (key, value) VALUES ('task_id_sequence', '{"counter":0,"lastId":"T000","checksum":"seed"}')`);
+        // Auto-recovery: detect empty database with available backups (T5188)
+        // Root cause: git-tracked WAL/SHM files get overwritten on branch switch,
+        // causing data loss when the WAL contained uncommitted writes.
+        await autoRecoverFromBackup(nativeDb, dbPath, cwd);
+        // Check if tasks.db or its WAL/SHM are dangerously tracked by git (ADR-013, T5158, T5188)
+        if (!_gitTrackingChecked) {
+            _gitTrackingChecked = true;
+            try {
+                const { execFileSync } = await import('node:child_process');
+                const gitCwd = resolve(dbPath, '..', '..');
+                const filesToCheck = [dbPath, dbPath + '-wal', dbPath + '-shm'];
+                const log = getLogger('sqlite');
+                for (const fileToCheck of filesToCheck) {
+                    try {
+                        execFileSync('git', ['ls-files', '--error-unmatch', fileToCheck], {
+                            cwd: gitCwd,
+                            stdio: 'pipe',
+                        });
+                        // If we get here, the file IS tracked — that's dangerous
+                        const basename = fileToCheck.split(/[\\/]/).pop();
+                        log.warn({ path: fileToCheck }, `${basename} is tracked by project git — this risks data loss on branch switch. ` +
+                            `Run: git rm --cached ${fileToCheck.replace(gitCwd + sep, '')} (see ADR-013, T5188)`);
+                    }
+                    catch {
+                        // Exit code 1 = not tracked = good
+                    }
+                }
+            }
+            catch {
+                // git not available, skip check
+            }
+        }
+        // Set singleton only after migrations complete
+        _db = db;
+        return db;
+    })();
+    try {
+        return await _initPromise;
+    }
+    finally {
+        _initPromise = null;
+    }
+}
+/**
+ * Resolve the path to the drizzle migrations folder.
+ * Works from both src/ (dev via tsx) and dist/ (compiled).
+ */
+export function resolveMigrationsFolder() {
+    const __filename = fileURLToPath(import.meta.url);
+    const __dirname = dirname(__filename);
+    // Both src/store/ and dist/store/ are 2 levels deep from package root
+    return join(__dirname, '..', '..', 'migrations', 'drizzle-tasks');
+}
+/**
+ * Check whether a table exists in the SQLite database.
+ */
+function tableExists(nativeDb, tableName) {
+    const result = nativeDb
+        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name=?")
+        .get(tableName);
+    return !!result;
+}
+/**
+ * Check if an error is a SQLite BUSY error (database locked by another process).
+ * node:sqlite throws native Error with message containing the SQLite error code.
+ * @task T5185
+ */
+export function isSqliteBusy(err) {
+    if (!(err instanceof Error))
+        return false;
+    const msg = err.message.toLowerCase();
+    return msg.includes('sqlite_busy') || msg.includes('database is locked');
+}
+/** Migration retry constants for SQLITE_BUSY handling (T5185). */
+const MAX_MIGRATION_RETRIES = 5;
+const MIGRATION_RETRY_BASE_DELAY_MS = 100;
+const MIGRATION_RETRY_MAX_DELAY_MS = 2000;
+/**
+ * Run drizzle migrations to create/update tables.
+ *
+ * Handles three cases:
+ * 1. New database — runs all migrations from scratch.
+ * 2. Existing database created by legacy createTablesIfNeeded() — bootstraps
+ *    the baseline migration as already applied, then runs remaining migrations.
+ * 3. Already-migrated database — runs only pending migrations.
+ *
+ * BEGIN IMMEDIATE acquires a RESERVED lock upfront, preventing concurrent
+ * migration runners from racing (T5173). If another process already holds a
+ * RESERVED lock, BEGIN IMMEDIATE throws SQLITE_BUSY. This function retries
+ * with exponential backoff + jitter to handle concurrent MCP server starts (T5185).
+ *
+ * @task T4837 - ADR-012 drizzle-kit migration system
+ * @task T5185 - Retry+backoff for SQLITE_BUSY during migrations
+ */
+function runMigrations(nativeDb, db) {
+    const migrationsFolder = resolveMigrationsFolder();
+    // If existing DB with pending migrations, create safety backup (cleo compat)
+    if (tableExists(nativeDb, 'tasks') && _dbPath) {
+        const backupPath = _dbPath.replace(/\.db$/, '-pre-cleo.db.bak');
+        if (!existsSync(backupPath)) {
+            try {
+                copyFileSync(_dbPath, backupPath);
+            }
+            catch { /* non-fatal */ }
+        }
+    }
+    // Bootstrap existing databases that predate drizzle migrations (ADR-012 Step D).
+    // These have tables (e.g., 'tasks') but no __drizzle_migrations record.
+    // Mark the baseline migration as already applied so migrate() doesn't
+    // try to re-create existing tables.
+    if (tableExists(nativeDb, 'tasks') && !tableExists(nativeDb, '__drizzle_migrations')) {
+        const migrations = readMigrationFiles({ migrationsFolder });
+        const baseline = migrations[0];
+        if (baseline) {
+            nativeDb.exec(`
+        CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+          id SERIAL PRIMARY KEY,
+          hash text NOT NULL,
+          created_at numeric
+        )
+      `);
+            nativeDb.exec(`INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${baseline.hash}', ${baseline.folderMillis})`);
+        }
+    }
+    // Run pending migrations via drizzle-orm/node-sqlite/migrator (synchronous).
+    // The new migrator handles its own transactions. T5185: retry on SQLITE_BUSY.
+    let lastError;
+    for (let attempt = 1; attempt <= MAX_MIGRATION_RETRIES; attempt++) {
+        try {
+            migrate(db, { migrationsFolder });
+            return;
+        }
+        catch (err) {
+            if (!isSqliteBusy(err) || attempt === MAX_MIGRATION_RETRIES) {
+                throw err;
+            }
+            lastError = err;
+            const delay = Math.min(MIGRATION_RETRY_BASE_DELAY_MS * 2 ** (attempt - 1) * (1 + Math.random() * 0.5), MIGRATION_RETRY_MAX_DELAY_MS);
+            Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, Math.round(delay));
+        }
+    }
+    /* c8 ignore next */
+    throw lastError;
+}
+/**
+ * Close the database connection and release resources.
+ */
+export function closeDb() {
+    if (_nativeDb) {
+        try {
+            if (_nativeDb.isOpen) {
+                _nativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nativeDb = null;
+    }
+    _db = null;
+    _dbPath = null;
+}
+/**
+ * Reset database singleton state without saving.
+ * Used during migrations when database file is deleted and recreated.
+ * Safe to call multiple times.
+ */
+export function resetDbState() {
+    if (_nativeDb) {
+        try {
+            if (_nativeDb.isOpen) {
+                _nativeDb.close();
+            }
+        }
+        catch {
+            // Ignore close errors
+        }
+        _nativeDb = null;
+    }
+    _db = null;
+    _dbPath = null;
+    _initPromise = null;
+}
+/**
+ * Get the schema version from the database.
+ */
+export async function getSchemaVersion(cwd) {
+    const db = await getDb(cwd);
+    const result = await db
+        .select()
+        .from(schema.schemaMeta)
+        .where(eq(schema.schemaMeta.key, 'schemaVersion'));
+    return result[0]?.value ?? null;
+}
+/**
+ * Check if the database file exists.
+ */
+export function dbExists(cwd) {
+    return existsSync(getDbPath(cwd));
+}
+/**
+ * Get the underlying node:sqlite DatabaseSync instance.
+ * Useful for direct PRAGMA calls or raw SQL operations.
+ * Returns null if the database hasn't been initialized.
+ */
+export function getNativeDb() {
+    return _nativeDb;
+}
+/**
+ * Get the underlying node:sqlite DatabaseSync instance for tasks.db.
+ * Alias for getNativeDb() — mirrors getBrainNativeDb() naming convention.
+ */
+export function getNativeTasksDb() {
+    return _nativeDb;
+}
+/**
+ * Re-export schema for external use.
+ */
+export { schema };
+/**
+ * Close ALL database singletons (tasks.db, brain.db, nexus.db).
+ *
+ * Must be called before deleting temp directories on Windows, where
+ * SQLite holds exclusive file handles on .db, .db-wal, and .db-shm files.
+ * Safe to call even if some databases were never opened.
+ *
+ * @task T5508
+ */
+export async function closeAllDatabases() {
+    // Close tasks.db
+    closeDb();
+    // Close brain.db (dynamic import to avoid circular deps)
+    try {
+        const { closeBrainDb } = await import('./brain-sqlite.js');
+        closeBrainDb();
+    }
+    catch {
+        /* module may not be loaded */
+    }
+    // Close nexus.db (dynamic import to avoid circular deps)
+    try {
+        const { closeNexusDb } = await import('./nexus-sqlite.js');
+        closeNexusDb();
+    }
+    catch {
+        /* module may not be loaded */
+    }
+}
+//# sourceMappingURL=sqlite.js.map