@cleocode/core 2026.4.18 → 2026.4.20

package/dist/init.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../src/init.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAgCH,sCAAsC;AACtC,MAAM,WAAW,WAAW;IAC1B,6BAA6B;IAC7B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,gCAAgC;IAChC,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,yCAAyC;IACzC,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,4DAA4D;IAC5D,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;;;;;OAQG;IACH,iBAAiB,CAAC,EAAE,OAAO,CAAC;CAC7B;AAED,oCAAoC;AACpC,MAAM,WAAW,UAAU;IACzB,WAAW,EAAE,OAAO,CAAC;IACrB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB;;;OAGG;IACH,cAAc,CAAC,EAAE;QACf,IAAI,EAAE,YAAY,GAAG,YAAY,CAAC;QAClC,WAAW,EAAE,MAAM,CAAC;QACpB,iBAAiB,EAAE,MAAM,CAAC;QAC1B,MAAM,EAAE,OAAO,CAAC;KACjB,CAAC;IACF;;;;OAIG;IACH,SAAS,CAAC,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACxD;AAaD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,CAiCnE;AAED;;;GAGG;AACH,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAqE9F;AAED;;;GAGG;AACH,wBAAsB,aAAa,CACjC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAAE,EAClB,SAAS,EAAE,MAAM,EAAE,GAClB,OAAO,CAAC,IAAI,CAAC,CAEf;AAED;;;;GAIG;AACH,wBAAsB,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CA+FzF;AAED;;;;;;GAMG;AACH,wBAAsB,qBAAqB,CACzC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,MAAM,EAAE,EACjB,QAAQ,EAAE,MAAM,EAAE,GACjB,OAAO,CAAC,IAAI,CAAC,CAuBf;AAID;;;;;;;;;;GAUG;AACH,wBAAsB,sBAAsB,CAC1C,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,MAAM,EAAE,EACjB,OAAO,EAAE,MAAM,EAAE,GAChB,OAAO,CAAC,IAAI,CAAC,CAiDf;AAID;;;;;GAKG;AACH,wBAAsB,UAAU,IAAI,OAAO,CAAC,UAAU,CAAC,CAwBtD;AAED;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,WAAW,CAAC,IAAI,GAAE,WAAgB,GAAG,OAAO,CAAC,UAAU,CAAC,CAoe7E;AAED;;;GAGG;AACH,wBAAgB,iBAAiB,IAAI,OAAO,CAE3C;AAED;;;;GAIG;AACH,wBAAsB,iBAAiB,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAAE,WAAW,EAAE,OAAO,CAAA;CAAE,CAAC,CAiB/F;AAED;;;;GAIG;AACH,wBAAsB,UAAU,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC,CAyBnF"}

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

@@ -1 +1 @@
-{"version":3,"file":"brain-sqlite.d.ts","sourceRoot":"","sources":["../../src/store/brain-sqlite.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAOH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAEhD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAGlE,OAAO,KAAK,WAAW,MAAM,mBAAmB,CAAC;AAcjD,gFAAgF;AAChF,eAAO,MAAM,oBAAoB,UAAU,CAAC;AAW5C;;GAEG;AACH,wBAAgB,cAAc,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,MAAM,CAEnD;AAED;;;;;;GAMG;AACH,wBAAgB,4BAA4B,IAAI,MAAM,CAMrD;AAoED;;GAEG;AACH,wBAAgB,gBAAgB,IAAI,OAAO,CAE1C;AAED;;;;;;;GAOG;AACH,wBAAsB,UAAU,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,kBAAkB,CAAC,OAAO,WAAW,CAAC,CAAC,CA0D9F;AAED;;GAEG;AACH,wBAAgB,YAAY,IAAI,IAAI,CAcnC;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,IAAI,IAAI,CAexC;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,IAAI,YAAY,GAAG,IAAI,CAEtD;AAED,YAAY,EAAE,kBAAkB,EAAE,CAAC;AACnC;;GAEG;AACH,OAAO,EAAE,WAAW,EAAE,CAAC"}
+{"version":3,"file":"brain-sqlite.d.ts","sourceRoot":"","sources":["../../src/store/brain-sqlite.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAOH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAEhD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAGlE,OAAO,KAAK,WAAW,MAAM,mBAAmB,CAAC;AAcjD,gFAAgF;AAChF,eAAO,MAAM,oBAAoB,UAAU,CAAC;AAW5C;;GAEG;AACH,wBAAgB,cAAc,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,MAAM,CAEnD;AAED;;;;;;GAMG;AACH,wBAAgB,4BAA4B,IAAI,MAAM,CAMrD;AAsED;;GAEG;AACH,wBAAgB,gBAAgB,IAAI,OAAO,CAE1C;AAED;;;;;;;GAOG;AACH,wBAAsB,UAAU,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,kBAAkB,CAAC,OAAO,WAAW,CAAC,CAAC,CA0D9F;AAED;;GAEG;AACH,wBAAgB,YAAY,IAAI,IAAI,CAcnC;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,IAAI,IAAI,CAexC;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,IAAI,YAAY,GAAG,IAAI,CAEtD;AAED,YAAY,EAAE,kBAAkB,EAAE,CAAC;AACnC;;GAEG;AACH,OAAO,EAAE,WAAW,EAAE,CAAC"}

package/dist/store/migration-manager.d.ts

@@ -40,7 +40,11 @@ export declare function createSafetyBackup(dbPath: string): void;
  * 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
+ * 3. Journal exists but is missing entries for migrations whose DDL has already been applied
+ *    (e.g., ALTER TABLE ADD COLUMN ran but journal entry was never written — happens when
+ *    migrations are cherry-picked from worktrees or the process crashes mid-migration).
+ *    Auto-inserts the missing journal entry so Drizzle skips the migration instead of
+ *    re-running ALTER TABLE and crashing on "duplicate column name".
  *
  * @param nativeDb - Native SQLite database handle
  * @param migrationsFolder - Path to the drizzle migrations folder
@@ -48,13 +52,29 @@ export declare function createSafetyBackup(dbPath: string): void;
  * @param logSubsystem - Logger subsystem name for reconciliation warnings
  */
 export declare function reconcileJournal(nativeDb: DatabaseSync, migrationsFolder: string, existenceTable: string, logSubsystem: string): void;
+/**
+ * Check whether an error is a SQLite "duplicate column name" error.
+ *
+ * These are thrown when an ALTER TABLE ADD COLUMN statement is re-executed
+ * after the column was already added (Scenario 3 in reconcileJournal).
+ */
+export declare function isDuplicateColumnError(err: unknown): boolean;
 /**
  * Run Drizzle migrations with SQLITE_BUSY retry and exponential backoff.
  *
+ * Also handles "duplicate column name" errors (Scenario 3): if Drizzle tries to
+ * re-apply a migration whose DDL columns already exist (journal entry missing),
+ * this function calls reconcileJournal again to insert the missing entry and
+ * retries migrate() once more. This is the belt-and-suspenders safety net for
+ * any partial migration that slips through the proactive reconcileJournal check.
+ *
  * @param db - Drizzle database instance
  * @param migrationsFolder - Path to the drizzle migrations folder
+ * @param nativeDb - Optional native SQLite handle for duplicate-column auto-reconcile
+ * @param existenceTable - Optional existence-check table name for auto-reconcile
+ * @param logSubsystem - Optional logger subsystem name for auto-reconcile warnings
  */
-export declare function migrateWithRetry(db: NodeSQLiteDatabase<any>, migrationsFolder: string): void;
+export declare function migrateWithRetry(db: NodeSQLiteDatabase<any>, migrationsFolder: string, nativeDb?: DatabaseSync, existenceTable?: string, logSubsystem?: string): void;
 /**
  * Ensure all required columns exist on a table.
  *

package/dist/store/migration-manager.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"migration-manager.d.ts","sourceRoot":"","sources":["../../src/store/migration-manager.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAGH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAEhD,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAIlE,sDAAsD;AACtD,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,6EAA6E;IAC7E,GAAG,EAAE,MAAM,CAAC;CACb;AAOD;;GAEG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,YAAY,EAAE,SAAS,EAAE,MAAM,GAAG,OAAO,CAK9E;AAED;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,OAAO,CAIlD;AAED;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CASvD;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,YAAY,EACtB,gBAAgB,EAAE,MAAM,EACxB,cAAc,EAAE,MAAM,EACtB,YAAY,EAAE,MAAM,GACnB,IAAI,CA8FN;AAED;;;;;GAKG;AACH,wBAAgB,sBAAsB,CAAC,GAAG,EAAE,OAAO,GAAG,OAAO,CAG5D;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,gBAAgB,CAE9B,EAAE,EAAE,kBAAkB,CAAC,GAAG,CAAC,EAC3B,gBAAgB,EAAE,MAAM,EACxB,QAAQ,CAAC,EAAE,YAAY,EACvB,cAAc,CAAC,EAAE,MAAM,EACvB,YAAY,CAAC,EAAE,MAAM,GACpB,IAAI,CAkCN;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,aAAa,CAC3B,QAAQ,EAAE,YAAY,EACtB,SAAS,EAAE,MAAM,EACjB,eAAe,EAAE,cAAc,EAAE,EACjC,YAAY,EAAE,MAAM,GACnB,IAAI,CAmBN"}

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

@@ -1 +1 @@
-{"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;AAKF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAYlE,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,CA2GpF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,IAAI,MAAM,CAQhD;AAED;;GAEG;AAGH,qDAAqD;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAsEtD;;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"}
+{"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;AAKF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAYlE,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,CA2GpF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,IAAI,MAAM,CAQhD;AAED;;GAEG;AAGH,qDAAqD;AACrD,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AAwEtD;;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/dist/tasks/add.d.ts.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cleocode/core",
-  "version": "2026.4.18",
+  "version": "2026.4.20",
   "description": "CLEO core business logic kernel — tasks, sessions, memory, orchestration, lifecycle, with bundled SQLite store",
   "type": "module",
   "main": "./dist/index.js",
@@ -36,12 +36,12 @@
     "write-file-atomic": "^7.0.1",
     "yaml": "^2.8.3",
     "zod": "^4.3.6",
-    "@cleocode/adapters": "2026.4.18",
-    "@cleocode/agents": "2026.4.18",
-    "@cleocode/contracts": "2026.4.18",
-    "@cleocode/lafs": "2026.4.18",
-    "@cleocode/caamp": "2026.4.18",
-    "@cleocode/skills": "2026.4.18"
+    "@cleocode/adapters": "2026.4.20",
+    "@cleocode/agents": "2026.4.20",
+    "@cleocode/caamp": "2026.4.20",
+    "@cleocode/contracts": "2026.4.20",
+    "@cleocode/lafs": "2026.4.20",
+    "@cleocode/skills": "2026.4.20"
   },
   "optionalDependencies": {
     "tree-sitter-c": "^0.24.1",

package/src/init.ts

@@ -828,6 +828,73 @@ export async function initProject(opts: InitOptions = {}): Promise<InitResult> {
     );
   }
 
+  // T441: Deploy starter CANT bundle (team + agents) to project-tier .cleo/cant/
+  // This gives the CANT bridge a working team topology on first `cleoos` run.
+  // Only deploys if .cleo/cant/ does not already contain .cant files (idempotent).
+  try {
+    const cantDir = join(cleoDir, 'cant');
+    const cantAgentsDir = join(cantDir, 'agents');
+    const hasCantFiles =
+      existsSync(cantDir) &&
+      readdirSync(cantDir, { recursive: true }).some(
+        (f) => typeof f === 'string' && f.endsWith('.cant'),
+      );
+
+    if (!hasCantFiles) {
+      // Resolve the starter-bundle from @cleocode/cleo-os package
+      let starterBundleSrc: string | null = null;
+      try {
+        const { createRequire } = await import('node:module');
+        const req = createRequire(import.meta.url);
+        const cleoOsPkgMain = req.resolve('@cleocode/cleo-os/package.json');
+        const cleoOsPkgRoot = dirname(cleoOsPkgMain);
+        const candidate = join(cleoOsPkgRoot, 'starter-bundle');
+        if (existsSync(candidate)) {
+          starterBundleSrc = candidate;
+        }
+      } catch {
+        // Not resolvable via require.resolve — try workspace fallbacks
+      }
+
+      if (!starterBundleSrc) {
+        const packageRoot = getPackageRoot();
+        const fallbacks = [
+          join(packageRoot, '..', 'cleo-os', 'starter-bundle'),
+          join(packageRoot, '..', '..', 'packages', 'cleo-os', 'starter-bundle'),
+        ];
+        starterBundleSrc = fallbacks.find((p) => existsSync(p)) ?? null;
+      }
+
+      if (starterBundleSrc) {
+        await mkdir(cantDir, { recursive: true });
+        await mkdir(cantAgentsDir, { recursive: true });
+
+        // Copy team.cant
+        const teamSrc = join(starterBundleSrc, 'team.cant');
+        const teamDst = join(cantDir, 'team.cant');
+        if (existsSync(teamSrc) && !existsSync(teamDst)) {
+          await copyFile(teamSrc, teamDst);
+        }
+
+        // Copy agent .cant files
+        const agentsSrc = join(starterBundleSrc, 'agents');
+        if (existsSync(agentsSrc)) {
+          const agentFiles = readdirSync(agentsSrc).filter((f) => f.endsWith('.cant'));
+          for (const agentFile of agentFiles) {
+            const dst = join(cantAgentsDir, agentFile);
+            if (!existsSync(dst)) {
+              await copyFile(join(agentsSrc, agentFile), dst);
+            }
+          }
+        }
+
+        created.push('starter-bundle: team + agent .cant files deployed to .cleo/cant/');
+      }
+    }
+  } catch (err) {
+    warnings.push(`Starter bundle deploy: ${err instanceof Error ? err.message : String(err)}`);
+  }
+
   // T283: Optional install of canonical CleoOS seed agent personas
   if (opts.installSeedAgents) {
     try {

package/src/store/__tests__/migration-reconcile.test.ts

@@ -0,0 +1,351 @@
+/**
+ * Tests for Scenario 3 in reconcileJournal: auto-reconciling partially-applied
+ * migrations whose DDL columns already exist in the database but whose journal
+ * entry was never written.
+ *
+ * Root cause: T417 migration (brain_observations.agent column) was cherry-picked
+ * from a worktree. The ALTER TABLE succeeded but the journal INSERT never ran,
+ * causing every subsequent `cleo observe` / `cleo memory find` to crash with
+ * "duplicate column name".
+ *
+ * @task T417
+ */
+
+import { mkdtemp, rm } from 'node:fs/promises';
+import { tmpdir } from 'node:os';
+import { dirname, join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+/** Resolve path to the drizzle-brain migrations folder relative to this test file. */
+function getBrainMigrationsFolder(): string {
+  // Test lives at: packages/core/src/store/__tests__/
+  // Migrations at: packages/core/migrations/drizzle-brain/
+  return join(__dirname, '..', '..', '..', 'migrations', 'drizzle-brain');
+}
+
+describe('reconcileJournal — Scenario 3 (T417: partially-applied migration)', () => {
+  let tempDir: string;
+
+  beforeEach(async () => {
+    tempDir = await mkdtemp(join(tmpdir(), 'cleo-reconcile-'));
+  });
+
+  afterEach(async () => {
+    await rm(tempDir, { recursive: true, force: true });
+  });
+
+  it('inserts a journal entry when the column exists but the entry is missing', async () => {
+    const { openNativeDatabase } = await import('../sqlite.js');
+    const { reconcileJournal } = await import('../migration-manager.js');
+
+    const dbPath = join(tempDir, 'brain-partial.db');
+    const nativeDb = openNativeDatabase(dbPath);
+    const migrationsFolder = getBrainMigrationsFolder();
+
+    // Simulate a brain.db that had the initial migration applied properly (schema
+    // exists, journal has the baseline hash) but the T417 migration was applied
+    // outside the journal (column added but journal entry never written).
+
+    // 1. Create the full initial schema from the initial migration SQL directly
+    //    (avoids pulling in the full Drizzle bootstrap; we just need the table).
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "brain_decisions" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "decision" text NOT NULL,
+        "rationale" text NOT NULL,
+        "confidence" text NOT NULL,
+        "outcome" text,
+        "alternatives_json" text,
+        "context_epic_id" text,
+        "context_task_id" text,
+        "context_phase" text,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+      CREATE TABLE IF NOT EXISTS "brain_observations" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "title" text NOT NULL,
+        "subtitle" text,
+        "narrative" text,
+        "facts_json" text,
+        "concepts_json" text,
+        "project" text,
+        "files_read_json" text,
+        "files_modified_json" text,
+        "source_session_id" text,
+        "source_type" text DEFAULT 'agent' NOT NULL,
+        "content_hash" text,
+        "discovery_tokens" integer,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+    `);
+
+    // 2. Manually apply the T417 ALTER TABLE (simulates cherry-pick from worktree).
+    nativeDb.exec('ALTER TABLE "brain_observations" ADD COLUMN "agent" text');
+
+    // 3. Create the journal table and insert ONLY the baseline + indexes migration
+    //    hashes — intentionally omitting the T417 hash.
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+        id SERIAL PRIMARY KEY,
+        hash text NOT NULL,
+        created_at numeric
+      )
+    `);
+    const { readMigrationFiles } = await import('drizzle-orm/migrator');
+    const allMigrations = readMigrationFiles({ migrationsFolder });
+
+    // Find the T417 migration by name
+    const t417 = allMigrations.find((m) => m.name.includes('t417'));
+    expect(t417).toBeDefined();
+
+    // Insert all migrations EXCEPT T417 into the journal
+    for (const m of allMigrations) {
+      if (m.hash === t417!.hash) continue;
+      nativeDb.exec(
+        `INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${m.hash}', ${m.folderMillis})`,
+      );
+    }
+
+    // 4. Verify the journal does NOT contain the T417 entry before reconcile.
+    const beforeEntries = nativeDb
+      .prepare('SELECT hash FROM "__drizzle_migrations"')
+      .all() as Array<{ hash: string }>;
+    expect(beforeEntries.some((e) => e.hash === t417!.hash)).toBe(false);
+
+    // 5. Run reconcileJournal — Scenario 3 must detect and insert the T417 entry.
+    reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
+
+    // 6. Journal must now contain the T417 entry.
+    const afterEntries = nativeDb
+      .prepare('SELECT hash FROM "__drizzle_migrations"')
+      .all() as Array<{ hash: string }>;
+    expect(afterEntries.some((e) => e.hash === t417!.hash)).toBe(true);
+
+    nativeDb.close();
+  });
+
+  it('does NOT insert a journal entry when the column is genuinely missing', async () => {
+    const { openNativeDatabase } = await import('../sqlite.js');
+    const { reconcileJournal } = await import('../migration-manager.js');
+
+    const dbPath = join(tempDir, 'brain-no-col.db');
+    const nativeDb = openNativeDatabase(dbPath);
+    const migrationsFolder = getBrainMigrationsFolder();
+
+    // Create the schema WITHOUT the agent column.
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "brain_decisions" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "decision" text NOT NULL,
+        "rationale" text NOT NULL,
+        "confidence" text NOT NULL,
+        "outcome" text,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL
+      );
+      CREATE TABLE IF NOT EXISTS "brain_observations" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "title" text NOT NULL,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL
+      );
+    `);
+
+    // Create the journal with baseline migrations but NOT T417.
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+        id SERIAL PRIMARY KEY,
+        hash text NOT NULL,
+        created_at numeric
+      )
+    `);
+    const { readMigrationFiles } = await import('drizzle-orm/migrator');
+    const allMigrations = readMigrationFiles({ migrationsFolder });
+    const t417 = allMigrations.find((m) => m.name.includes('t417'));
+    expect(t417).toBeDefined();
+
+    for (const m of allMigrations) {
+      if (m.hash === t417!.hash) continue;
+      nativeDb.exec(
+        `INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${m.hash}', ${m.folderMillis})`,
+      );
+    }
+
+    // Run reconcileJournal — since the column does NOT exist, Scenario 3 must
+    // NOT insert the T417 entry (leave it for Drizzle to run normally).
+    reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
+
+    const entries = nativeDb.prepare('SELECT hash FROM "__drizzle_migrations"').all() as Array<{
+      hash: string;
+    }>;
+    expect(entries.some((e) => e.hash === t417!.hash)).toBe(false);
+
+    nativeDb.close();
+  });
+
+  it('migrateWithRetry does not throw after reconcileJournal inserts the missing entry', async () => {
+    const { openNativeDatabase } = await import('../sqlite.js');
+    const { reconcileJournal, migrateWithRetry } = await import('../migration-manager.js');
+    const { drizzle } = await import('drizzle-orm/node-sqlite');
+    const brainSchema = await import('../brain-schema.js');
+
+    const dbPath = join(tempDir, 'brain-full.db');
+    const nativeDb = openNativeDatabase(dbPath);
+    const migrationsFolder = getBrainMigrationsFolder();
+
+    // Build the complete brain schema with the agent column already present.
+    // This mirrors a real production brain.db after T417 was cherry-picked.
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "brain_decisions" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "decision" text NOT NULL,
+        "rationale" text NOT NULL,
+        "confidence" text NOT NULL,
+        "outcome" text,
+        "alternatives_json" text,
+        "context_epic_id" text,
+        "context_task_id" text,
+        "context_phase" text,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+      CREATE TABLE IF NOT EXISTS "brain_learnings" (
+        "id" text PRIMARY KEY,
+        "insight" text NOT NULL,
+        "source" text NOT NULL,
+        "confidence" real NOT NULL,
+        "actionable" integer DEFAULT false NOT NULL,
+        "application" text,
+        "applicable_types_json" text,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+      CREATE TABLE IF NOT EXISTS "brain_memory_links" (
+        "memory_type" text NOT NULL,
+        "memory_id" text NOT NULL,
+        "task_id" text NOT NULL,
+        "link_type" text NOT NULL,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        CONSTRAINT "brain_memory_links_pk" PRIMARY KEY("memory_type", "memory_id", "task_id", "link_type")
+      );
+      CREATE TABLE IF NOT EXISTS "brain_observations" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "title" text NOT NULL,
+        "subtitle" text,
+        "narrative" text,
+        "facts_json" text,
+        "concepts_json" text,
+        "project" text,
+        "files_read_json" text,
+        "files_modified_json" text,
+        "source_session_id" text,
+        "source_type" text DEFAULT 'agent' NOT NULL,
+        "content_hash" text,
+        "discovery_tokens" integer,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+      CREATE TABLE IF NOT EXISTS "brain_page_edges" (
+        "from_id" text NOT NULL,
+        "to_id" text NOT NULL,
+        "edge_type" text NOT NULL,
+        "weight" real DEFAULT 1,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        CONSTRAINT "brain_page_edges_pk" PRIMARY KEY("from_id", "to_id", "edge_type")
+      );
+      CREATE TABLE IF NOT EXISTS "brain_page_nodes" (
+        "id" text PRIMARY KEY,
+        "node_type" text NOT NULL,
+        "label" text NOT NULL,
+        "metadata_json" text,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL
+      );
+      CREATE TABLE IF NOT EXISTS "brain_patterns" (
+        "id" text PRIMARY KEY,
+        "type" text NOT NULL,
+        "pattern" text NOT NULL,
+        "context" text NOT NULL,
+        "frequency" integer DEFAULT 1 NOT NULL,
+        "success_rate" real,
+        "impact" text,
+        "anti_pattern" text,
+        "mitigation" text,
+        "examples_json" text DEFAULT '[]',
+        "extracted_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text
+      );
+      CREATE TABLE IF NOT EXISTS "brain_schema_meta" (
+        "key" text PRIMARY KEY,
+        "value" text NOT NULL
+      );
+      CREATE TABLE IF NOT EXISTS "brain_sticky_notes" (
+        "id" text PRIMARY KEY,
+        "content" text NOT NULL,
+        "created_at" text DEFAULT (datetime('now')) NOT NULL,
+        "updated_at" text,
+        "tags_json" text,
+        "status" text DEFAULT 'active' NOT NULL,
+        "converted_to_json" text,
+        "color" text,
+        "priority" text,
+        "source_type" text DEFAULT 'sticky-note'
+      );
+    `);
+
+    // T417: agent column already applied out-of-band.
+    nativeDb.exec('ALTER TABLE "brain_observations" ADD COLUMN "agent" text');
+
+    // Journal: all migrations except T417.
+    nativeDb.exec(`
+      CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+        id SERIAL PRIMARY KEY,
+        hash text NOT NULL,
+        created_at numeric
+      )
+    `);
+    const { readMigrationFiles } = await import('drizzle-orm/migrator');
+    const allMigrations = readMigrationFiles({ migrationsFolder });
+    const t417 = allMigrations.find((m) => m.name.includes('t417'));
+    expect(t417).toBeDefined();
+
+    for (const m of allMigrations) {
+      if (m.hash === t417!.hash) continue;
+      nativeDb.exec(
+        `INSERT INTO "__drizzle_migrations" ("hash", "created_at") VALUES ('${m.hash}', ${m.folderMillis})`,
+      );
+    }
+
+    // reconcileJournal fills in the missing T417 entry.
+    reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
+
+    // migrateWithRetry must NOT throw "duplicate column name".
+    const db = drizzle(nativeDb, { schema: brainSchema });
+    expect(() =>
+      migrateWithRetry(db, migrationsFolder, nativeDb, 'brain_decisions', 'brain'),
+    ).not.toThrow();
+
+    nativeDb.close();
+  });
+
+  it('isDuplicateColumnError correctly identifies duplicate column errors', async () => {
+    const { isDuplicateColumnError } = await import('../migration-manager.js');
+
+    expect(isDuplicateColumnError(new Error('duplicate column name: agent'))).toBe(true);
+    expect(isDuplicateColumnError(new Error('DUPLICATE COLUMN NAME: foo'))).toBe(true);
+    expect(isDuplicateColumnError(new Error('Duplicate column name in table'))).toBe(true);
+    expect(isDuplicateColumnError(new Error('SQLITE_BUSY: database is locked'))).toBe(false);
+    expect(isDuplicateColumnError(new Error('no such table: tasks'))).toBe(false);
+    expect(isDuplicateColumnError('not an error')).toBe(false);
+    expect(isDuplicateColumnError(null)).toBe(false);
+  });
+});

package/src/store/brain-sqlite.ts

@@ -92,8 +92,10 @@ function runBrainMigrations(
   // Bootstrap baseline + reconcile stale journal entries
   reconcileJournal(nativeDb, migrationsFolder, 'brain_decisions', 'brain');
 
-  // Run pending migrations with SQLITE_BUSY retry
-  migrateWithRetry(db, migrationsFolder);
+  // 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');
 }
 
 /**