@cleocode/core 2026.3.60 → 2026.3.61

package/dist/internal.d.ts

@@ -37,6 +37,7 @@ export { analyzeChangeImpact, analyzeTaskImpact, calculateBlastRadius, predictIm
 export { extractPatternsFromHistory, matchPatterns, storeDetectedPattern, updatePatternStats, } from './intelligence/patterns.js';
 export { calculateTaskRisk, gatherLearningContext, predictValidationOutcome, } from './intelligence/prediction.js';
 export type { AffectedTask, BlastRadius, BlastRadiusSeverity, ChangeImpact, ChangeType, DetectedPattern, ImpactAssessment, ImpactedTask, ImpactReport, LearningContext, PatternExtractionOptions, PatternMatch, PatternStatsUpdate, RiskAssessment, RiskFactor, ValidationPrediction, } from './intelligence/types.js';
+export { type AddIssueParams, type AddIssueResult, addIssue } from './issue/create.js';
 export { collectDiagnostics } from './issue/diagnostics.js';
 export { computeDelay, type RetryablePredicate, type RetryContext, type RetryOptions, withRetry as withRetryShared, } from './lib/retry.js';
 export { addChain, advanceInstance, createInstance, listChains, showChain, } from './lifecycle/chain-store.js';

package/dist/internal.d.ts.map

@@ -1 +1 @@
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package/dist/repair.d.ts

@@ -22,6 +22,13 @@ export declare function repairMissingSizes(cwd: string | undefined, dryRun: bool
  * Operates directly on the SQLite tasks table.
  */
 export declare function repairMissingCompletedAt(cwd: string | undefined, dryRun: boolean): Promise<RepairAction>;
+/**
+ * Detect and add missing required columns on the tasks table.
+ * Uses PRAGMA table_info to check actual schema vs required columns.
+ *
+ * @see https://github.com/anthropics/cleo/issues/63
+ */
+export declare function repairMissingColumns(cwd: string | undefined, dryRun: boolean): Promise<RepairAction>;
 /**
  * Run all repair functions.
  * Returns all actions taken (or previewed in dry-run mode).

package/dist/repair.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"repair.d.ts","sourceRoot":"","sources":["../src/repair.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,0CAA0C;AAC1C,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS,CAAC;IAC1C,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,CAAC,CA+BvB;AAED;;;GAGG;AACH,wBAAsB,wBAAwB,CAC5C,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,CAAC,CA0CvB;AAED;;;GAGG;AACH,wBAAsB,aAAa,CACjC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,EAAE,CAAC,CAMzB"}
+{"version":3,"file":"repair.d.ts","sourceRoot":"","sources":["../src/repair.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,0CAA0C;AAC1C,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,SAAS,GAAG,SAAS,GAAG,SAAS,CAAC;IAC1C,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,CAAC,CA+BvB;AAED;;;GAGG;AACH,wBAAsB,wBAAwB,CAC5C,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,CAAC,CA0CvB;AAED;;;;;GAKG;AACH,wBAAsB,oBAAoB,CACxC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,CAAC,CAuCvB;AAED;;;GAGG;AACH,wBAAsB,aAAa,CACjC,GAAG,EAAE,MAAM,GAAG,SAAS,EACvB,MAAM,EAAE,OAAO,GACd,OAAO,CAAC,YAAY,EAAE,CAAC,CAOzB"}

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

@@ -1 +1 @@
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+{"version":3,"file":"sqlite.d.ts","sourceRoot":"","sources":["../../src/store/sqlite.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAOH,OAAO,KAAK,EAAE,YAAY,IAAI,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAGrE,KAAK,YAAY,GAAG,iBAAiB,CAAC;AACtC,QAAA,MAAQ,YAAY,wGAC8D,YACjF,CAAC;AAMF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAMlE,OAAO,KAAK,MAAM,MAAM,mBAAmB,CAAC;AAE5C;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAChC,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IACR,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B,GACA,YAAY,CAiEd;AAKD,0EAA0E;AAC1E,eAAO,MAAM,qBAAqB,UAAU,CAAC;AAY7C;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,MAAM,CAE9C;AAyHD;;;;;;;GAOG;AACH,wBAAsB,KAAK,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,kBAAkB,CAAC,OAAO,MAAM,CAAC,CAAC,CA2FpF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,IAAI,MAAM,CAQhD;AAYD;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,OAAO,CAIlD;AAsJD;;GAEG;AACH,wBAAgB,OAAO,IAAI,IAAI,CAc9B;AAED;;;;GAIG;AACH,wBAAgB,YAAY,IAAI,IAAI,CAcnC;AAED;;GAEG;AACH,wBAAsB,gBAAgB,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAQ3E;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED;;;;GAIG;AACH,wBAAgB,WAAW,IAAI,YAAY,GAAG,IAAI,CAEjD;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,IAAI,YAAY,GAAG,IAAI,CAEtD;AAED,YAAY,EAAE,kBAAkB,EAAE,CAAC;AACnC;;GAEG;AACH,OAAO,EAAE,MAAM,EAAE,CAAC;AAElB;;;;;;;;GAQG;AACH,wBAAsB,iBAAiB,IAAI,OAAO,CAAC,IAAI,CAAC,CAmBvD"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cleocode/core",
-  "version": "2026.3.60",
+  "version": "2026.3.61",
   "description": "CLEO core business logic kernel — tasks, sessions, memory, orchestration, lifecycle, with bundled SQLite store",
   "type": "module",
   "main": "./dist/index.js",
@@ -36,10 +36,10 @@
     "write-file-atomic": "^6.0.0",
     "yaml": "^2.8.2",
     "zod": "^3.25.76",
-    "@cleocode/adapters": "2026.3.60",
-    "@cleocode/agents": "2026.3.60",
-    "@cleocode/skills": "2026.3.60",
-    "@cleocode/contracts": "2026.3.60"
+    "@cleocode/adapters": "2026.3.61",
+    "@cleocode/contracts": "2026.3.61",
+    "@cleocode/agents": "2026.3.61",
+    "@cleocode/skills": "2026.3.61"
   },
   "engines": {
     "node": ">=24.0.0"

package/src/internal.ts

@@ -98,7 +98,7 @@ export type {
   RiskFactor,
   ValidationPrediction,
 } from './intelligence/types.js';
-
+export { type AddIssueParams, type AddIssueResult, addIssue } from './issue/create.js';
 // Issue
 export { collectDiagnostics } from './issue/diagnostics.js';
 // Lib — shared primitives

package/src/repair.ts

@@ -105,6 +105,56 @@ export async function repairMissingCompletedAt(
   };
 }
 
+/**
+ * Detect and add missing required columns on the tasks table.
+ * Uses PRAGMA table_info to check actual schema vs required columns.
+ *
+ * @see https://github.com/anthropics/cleo/issues/63
+ */
+export async function repairMissingColumns(
+  cwd: string | undefined,
+  dryRun: boolean,
+): Promise<RepairAction> {
+  const { getDb } = await import('./store/sqlite.js');
+  const db = await getDb(cwd);
+
+  // getDb() already calls ensureRequiredColumns(), so if we get here
+  // the column should exist. But we still report the action for visibility.
+  const { sql } = await import('drizzle-orm');
+  const columns = db.all<{ name: string }>(sql`PRAGMA table_info(tasks)`);
+  const existingCols = new Set(columns.map((c: { name: string }) => c.name));
+
+  const missingCols = ['pipeline_stage'].filter((c) => !existingCols.has(c));
+
+  if (missingCols.length === 0) {
+    return {
+      action: 'fix_missing_columns',
+      status: 'skipped',
+      details: 'All required columns present on tasks table',
+    };
+  }
+
+  if (dryRun) {
+    return {
+      action: 'fix_missing_columns',
+      status: 'preview',
+      details: `Would add missing column(s): ${missingCols.join(', ')}`,
+    };
+  }
+
+  // Columns should already be added by ensureRequiredColumns() in getDb(),
+  // but apply again defensively.
+  for (const col of missingCols) {
+    db.run(sql.raw(`ALTER TABLE tasks ADD COLUMN ${col} text`));
+  }
+
+  return {
+    action: 'fix_missing_columns',
+    status: 'applied',
+    details: `Added missing column(s): ${missingCols.join(', ')}`,
+  };
+}
+
 /**
  * Run all repair functions.
  * Returns all actions taken (or previewed in dry-run mode).
@@ -113,9 +163,10 @@ export async function runAllRepairs(
   cwd: string | undefined,
   dryRun: boolean,
 ): Promise<RepairAction[]> {
-  const [sizes, completedAt] = await Promise.all([
+  const [sizes, completedAt, columns] = await Promise.all([
     repairMissingSizes(cwd, dryRun),
     repairMissingCompletedAt(cwd, dryRun),
+    repairMissingColumns(cwd, dryRun),
   ]);
-  return [sizes, completedAt];
+  return [sizes, completedAt, columns];
 }

package/src/store/sqlite.ts

@@ -462,18 +462,48 @@ function runMigrations(nativeDb: DatabaseSync, db: NodeSQLiteDatabase<typeof sch
     }
   }
 
+  // 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() as Array<{
+      hash: string;
+    }>;
+    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.
-  let lastError: unknown;
   for (let attempt = 1; attempt <= MAX_MIGRATION_RETRIES; attempt++) {
     try {
       migrate(db, { migrationsFolder });
-      return;
+      break;
     } 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,
@@ -481,8 +511,45 @@ function runMigrations(nativeDb: DatabaseSync, db: NodeSQLiteDatabase<typeof sch
       Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, Math.round(delay));
     }
   }
-  /* c8 ignore next */
-  throw lastError;
+
+  // 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: Array<{ name: string; ddl: string }> = [
+  { 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: DatabaseSync): void {
+  if (!tableExists(nativeDb, 'tasks')) return;
+
+  const columns = nativeDb.prepare('PRAGMA table_info(tasks)').all() as Array<{ name: string }>;
+  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}`);
+    }
+  }
 }
 
 /**