@cleocode/core 2026.3.68 → 2026.3.70

package/dist/store/migration-manager.js

@@ -0,0 +1,151 @@
+/**
+ * Unified migration manager for SQLite databases.
+ *
+ * Consolidates duplicated reconciliation, bootstrap, retry, and column-safety
+ * logic that was previously copy-pasted between sqlite.ts (tasks.db) and
+ * brain-sqlite.ts (brain.db). Both modules now delegate to these shared functions.
+ *
+ * @task T132
+ * @see https://github.com/anthropics/cleo/issues/82
+ * @see https://github.com/anthropics/cleo/issues/63
+ * @see https://github.com/anthropics/cleo/issues/65
+ */
+import { copyFileSync, existsSync } from 'node:fs';
+import { readMigrationFiles } from 'drizzle-orm/migrator';
+import { migrate } from 'drizzle-orm/node-sqlite/migrator';
+import { getLogger } from '../logger.js';
+/** 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;
+/**
+ * Check whether a table exists in a SQLite database.
+ */
+export 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');
+}
+/**
+ * Create a pre-migration safety backup of the database file.
+ *
+ * Only creates the backup once (idempotent). Non-fatal on failure.
+ */
+export function createSafetyBackup(dbPath) {
+    const backupPath = dbPath.replace(/\.db$/, '-pre-cleo.db.bak');
+    if (!existsSync(backupPath)) {
+        try {
+            copyFileSync(dbPath, backupPath);
+        }
+        catch {
+            /* non-fatal */
+        }
+    }
+}
+/**
+ * Bootstrap and reconcile the Drizzle migration journal.
+ *
+ * Handles three scenarios:
+ * 1. Tables exist but no __drizzle_migrations — bootstrap baseline as applied
+ * 2. Journal has orphaned hashes (from older CLEO version) — clear and re-mark all as applied
+ * 3. Journal is healthy — no-op
+ *
+ * @param nativeDb - Native SQLite database handle
+ * @param migrationsFolder - Path to the drizzle migrations folder
+ * @param existenceTable - A table name used to detect if the DB has data (e.g., 'tasks' or 'brain_decisions')
+ * @param logSubsystem - Logger subsystem name for reconciliation warnings
+ */
+export function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsystem) {
+    // Scenario 1: Tables exist but no migration journal — bootstrap baseline
+    if (tableExists(nativeDb, existenceTable) && !tableExists(nativeDb, '__drizzle_migrations')) {
+        const migrations = readMigrationFiles({ migrationsFolder });
+        const baseline = migrations[0];
+        if (baseline) {
+            nativeDb.exec(`
+        CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+          id SERIAL PRIMARY KEY,
+          hash text NOT NULL,
+          created_at numeric
+        )
+      `);
+            nativeDb.exec(`INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${baseline.hash}', ${baseline.folderMillis})`);
+        }
+    }
+    // Scenario 2: Journal has orphaned entries from a previous CLEO version
+    if (tableExists(nativeDb, '__drizzle_migrations') && tableExists(nativeDb, existenceTable)) {
+        const localMigrations = readMigrationFiles({ migrationsFolder });
+        const localHashes = new Set(localMigrations.map((m) => m.hash));
+        const dbEntries = nativeDb.prepare('SELECT hash FROM "__drizzle_migrations"').all();
+        const hasOrphanedEntries = dbEntries.some((e) => !localHashes.has(e.hash));
+        if (hasOrphanedEntries) {
+            const log = getLogger(logSubsystem);
+            log.warn({ orphaned: dbEntries.filter((e) => !localHashes.has(e.hash)).length }, `Detected stale migration journal entries from a previous CLEO version. Reconciling.`);
+            nativeDb.exec('DELETE FROM "__drizzle_migrations"');
+            for (const m of localMigrations) {
+                nativeDb.exec(`INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${m.hash}', ${m.folderMillis})`);
+            }
+        }
+    }
+}
+/**
+ * Run Drizzle migrations with SQLITE_BUSY retry and exponential backoff.
+ *
+ * @param db - Drizzle database instance
+ * @param migrationsFolder - Path to the drizzle migrations folder
+ */
+// biome-ignore lint/suspicious/noExplicitAny: Drizzle's NodeSQLiteDatabase is generic — accepting any schema avoids coupling to a specific schema type
+export function migrateWithRetry(db, migrationsFolder) {
+    for (let attempt = 1; attempt <= MAX_MIGRATION_RETRIES; attempt++) {
+        try {
+            migrate(db, { migrationsFolder });
+            return;
+        }
+        catch (err) {
+            if (!isSqliteBusy(err) || attempt === MAX_MIGRATION_RETRIES) {
+                throw err;
+            }
+            const delay = Math.min(MIGRATION_RETRY_BASE_DELAY_MS * 2 ** (attempt - 1) * (1 + Math.random() * 0.5), MIGRATION_RETRY_MAX_DELAY_MS);
+            Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, Math.round(delay));
+        }
+    }
+}
+/**
+ * Ensure all required columns exist on a table.
+ *
+ * Uses PRAGMA table_info to inspect the schema and adds any missing columns
+ * via ALTER TABLE ADD COLUMN. Safety net for databases where Drizzle migrations
+ * could not run due to journal corruption or version skew.
+ *
+ * @param nativeDb - Native SQLite database handle
+ * @param tableName - Table to check (e.g., 'tasks')
+ * @param requiredColumns - Columns that must exist
+ * @param logSubsystem - Logger subsystem name
+ */
+export function ensureColumns(nativeDb, tableName, requiredColumns, logSubsystem) {
+    if (!tableExists(nativeDb, tableName))
+        return;
+    if (requiredColumns.length === 0)
+        return;
+    const columns = nativeDb.prepare(`PRAGMA table_info(${tableName})`).all();
+    const existingCols = new Set(columns.map((c) => c.name));
+    for (const req of requiredColumns) {
+        if (!existingCols.has(req.name)) {
+            const log = getLogger(logSubsystem);
+            log.warn({ column: req.name }, `Adding missing column ${tableName}.${req.name} via ALTER TABLE`);
+            nativeDb.exec(`ALTER TABLE ${tableName} ADD COLUMN ${req.name} ${req.ddl}`);
+        }
+    }
+}
+//# sourceMappingURL=migration-manager.js.map

package/dist/store/migration-manager.js.map

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

@@ -1 +1 @@
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package/dist/store/sqlite.js

@@ -21,11 +21,10 @@ 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 { createSafetyBackup, ensureColumns, migrateWithRetry, reconcileJournal, tableExists, } from './migration-manager.js';
 import { listSqliteBackups } from './sqlite-backup.js';
 import * as schema from './tasks-schema.js';
 /**
@@ -302,149 +301,32 @@ export function resolveMigrationsFolder() {
 /**
  * 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;
+// tableExists, isSqliteBusy, retry constants — delegated to migration-manager.ts (T132)
+/** Re-export isSqliteBusy for external consumers. */
+export { isSqliteBusy } from './migration-manager.js';
+const REQUIRED_TASK_COLUMNS = [{ name: 'pipeline_stage', ddl: 'text' }];
 /**
  * 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).
+ * Delegates to shared migration-manager.ts for journal reconciliation,
+ * retry logic, and column safety. See T132 for consolidation rationale.
  *
  * @task T4837 - ADR-012 drizzle-kit migration system
  * @task T5185 - Retry+backoff for SQLITE_BUSY during migrations
+ * @task T132 - Unified migration system
  */
 function runMigrations(nativeDb, db) {
     const migrationsFolder = resolveMigrationsFolder();
-    // If existing DB with pending migrations, create safety backup (cleo compat)
+    // Safety backup before any migration work
     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}', ${baseline.folderMillis})`);
-        }
-    }
-    // Fix #63: Reconcile stale migration journal entries from older CLEO versions.
-    // When the DB has __drizzle_migrations entries whose hashes don't match ANY
-    // local migration file, drizzle's migrate() either throws or tries to re-run
-    // all migrations (causing "table already exists" errors). Fix by clearing stale
-    // entries and marking all local migrations as applied (tables already exist),
-    // then relying on ensureRequiredColumns() to patch any schema gaps.
-    if (tableExists(nativeDb, '__drizzle_migrations') && tableExists(nativeDb, 'tasks')) {
-        const localMigrations = readMigrationFiles({ migrationsFolder });
-        const localHashes = new Set(localMigrations.map((m) => m.hash));
-        const dbEntries = nativeDb.prepare('SELECT hash FROM "__drizzle_migrations"').all();
-        const hasOrphanedEntries = dbEntries.some((e) => !localHashes.has(e.hash));
-        if (hasOrphanedEntries) {
-            const log = getLogger('sqlite');
-            log.warn({ orphaned: dbEntries.filter((e) => !localHashes.has(e.hash)).length }, 'Detected stale migration journal entries from a previous CLEO version. Reconciling.');
-            // Clear all entries and mark every local migration as applied.
-            // The existing tables were created by the previous version's migrations,
-            // so we skip re-running them. ensureRequiredColumns() fills any schema gaps.
-            nativeDb.exec('DELETE FROM "__drizzle_migrations"');
-            for (const m of localMigrations) {
-                nativeDb.exec(`INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${m.hash}', ${m.folderMillis})`);
-            }
-        }
-    }
-    // Run pending migrations via drizzle-orm/node-sqlite/migrator (synchronous).
-    // The new migrator handles its own transactions. T5185: retry on SQLITE_BUSY.
-    for (let attempt = 1; attempt <= MAX_MIGRATION_RETRIES; attempt++) {
-        try {
-            migrate(db, { migrationsFolder });
-            break;
-        }
-        catch (err) {
-            if (!isSqliteBusy(err) || attempt === MAX_MIGRATION_RETRIES) {
-                throw 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));
-        }
-    }
-    // Fix #63: Defensive column safety net — add any columns the schema expects
-    // but that are missing from the actual table. This catches gaps from stale
-    // migration journals, partial migrations, or version skew.
-    ensureRequiredColumns(nativeDb);
-}
-/**
- * Required columns that MUST exist on the tasks table.
- * Maps column name → ALTER TABLE ADD COLUMN DDL suffix.
- * Only TEXT columns with no constraints are safe for ALTER TABLE ADD in SQLite.
- *
- * @see https://github.com/anthropics/cleo/issues/63
- */
-const REQUIRED_TASK_COLUMNS = [
-    { name: 'pipeline_stage', ddl: 'text' },
-];
-/**
- * Ensure all required columns exist on the tasks table.
- * Uses PRAGMA table_info to inspect the schema and adds any missing columns
- * via ALTER TABLE ADD COLUMN. This is a safety net for databases where
- * Drizzle migrations could not run due to journal corruption or version skew.
- *
- * @see https://github.com/anthropics/cleo/issues/63
- */
-function ensureRequiredColumns(nativeDb) {
-    if (!tableExists(nativeDb, 'tasks'))
-        return;
-    const columns = nativeDb.prepare('PRAGMA table_info(tasks)').all();
-    const existingCols = new Set(columns.map((c) => c.name));
-    for (const req of REQUIRED_TASK_COLUMNS) {
-        if (!existingCols.has(req.name)) {
-            const log = getLogger('sqlite');
-            log.warn({ column: req.name }, `Adding missing column tasks.${req.name} via ALTER TABLE`);
-            nativeDb.exec(`ALTER TABLE tasks ADD COLUMN ${req.name} ${req.ddl}`);
-        }
+        createSafetyBackup(_dbPath);
     }
+    // Bootstrap baseline + reconcile stale journal entries
+    reconcileJournal(nativeDb, migrationsFolder, 'tasks', 'sqlite');
+    // Run pending migrations with SQLITE_BUSY retry
+    migrateWithRetry(db, migrationsFolder);
+    // Defensive column safety net
+    ensureColumns(nativeDb, 'tasks', REQUIRED_TASK_COLUMNS, 'sqlite');
 }
 /**
  * Close the database connection and release resources.

package/dist/store/sqlite.js.map

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