fix: preserve install markers for Codex plugin roots

src/npx-cli/commands/install.ts

@@ -1603,7 +1603,6 @@ async function runInstallCommandInner(options: InstallOptions, summary: InstallS
             } finally {
               stopHeartbeat();
             }
-            writeInstallMarker(cacheDir, version, bunVersion, uvVersion);
           }
           return `Runtime ready (Bun ${bunVersion}, uv ${uvVersion}) ${pc.green('OK')}`;
         },
@@ -1638,6 +1637,13 @@ async function runInstallCommandInner(options: InstallOptions, summary: InstallS
     }
 
     await runTasks(tasks);
+
+    if (installedBunVersion && installedUvVersion) {
+      writeInstallMarker(cacheDir, version, installedBunVersion, installedUvVersion);
+      if (needsMarketplace && existsSync(join(marketplaceDirectory(), 'plugin', 'package.json'))) {
+        writeInstallMarker(marketplaceDirectory(), version, installedBunVersion, installedUvVersion);
+      }
+    }
   }
 
   const failedIDEs = await setupIDEs(selectedIDEs, summary);
@@ -1908,6 +1914,9 @@ export async function runRepairCommand(): Promise<void> {
         const { bunPath } = await ensureBun();
         await installPluginDependencies(cacheDir, bunPath);
         writeInstallMarker(cacheDir, version, bunVersion, uvVersion);
+        if (existsSync(join(marketplaceDirectory(), 'plugin', 'package.json'))) {
+          writeInstallMarker(marketplaceDirectory(), version, bunVersion, uvVersion);
+        }
         return `Runtime ready (Bun ${bunVersion}, uv ${uvVersion}) ${pc.green('OK')}`;
       },
     },

src/npx-cli/install/setup-runtime.ts

@@ -67,7 +67,15 @@ const LEGACY_VERSION_MARKER_RE =
   /^v?\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?(?:\+[0-9A-Za-z.-]+)?$/;
 
 function markerPath(targetDir: string): string {
-  return join(targetDir, '.install-version');
+  return join(resolveInstallTargetDir(targetDir), '.install-version');
+}
+
+function resolveInstallTargetDir(targetDir: string): string {
+  const bundledPluginRoot = join(targetDir, 'plugin');
+  if (existsSync(join(bundledPluginRoot, 'package.json'))) {
+    return bundledPluginRoot;
+  }
+  return targetDir;
 }
 
 function getBunPath(): string | null {
@@ -467,7 +475,8 @@ export function writeInstallMarker(
 }
 
 export function isInstallCurrent(targetDir: string, expectedVersion: string): boolean {
-  if (!existsSync(join(targetDir, 'node_modules'))) return false;
+  const installDir = resolveInstallTargetDir(targetDir);
+  if (!existsSync(join(installDir, 'node_modules'))) return false;
   const marker = readInstallMarker(targetDir);
   if (!marker) return false;
   if (marker.version !== expectedVersion) return false;

src/services/sqlite/SessionStore.ts

@@ -460,8 +460,6 @@ export class SessionStore {
       CREATE INDEX IF NOT EXISTS idx_sdk_sessions_project ON sdk_sessions(project);
       CREATE INDEX IF NOT EXISTS idx_sdk_sessions_status ON sdk_sessions(status);
       CREATE INDEX IF NOT EXISTS idx_sdk_sessions_started ON sdk_sessions(started_at_epoch DESC);
-      CREATE INDEX IF NOT EXISTS idx_sdk_sessions_platform_source ON sdk_sessions(platform_source);
-      CREATE UNIQUE INDEX IF NOT EXISTS ux_sdk_sessions_platform_content ON sdk_sessions(platform_source, content_session_id);
 
       CREATE TABLE IF NOT EXISTS observations (
         id INTEGER PRIMARY KEY AUTOINCREMENT,
@@ -501,6 +499,13 @@ export class SessionStore {
       CREATE INDEX IF NOT EXISTS idx_session_summaries_created ON session_summaries(created_at_epoch DESC);
     `);
 
+    const sdkSessionColumns = this.db.query('PRAGMA table_info(sdk_sessions)').all() as TableColumnInfo[];
+    const hasPlatformSource = sdkSessionColumns.some(col => col.name === 'platform_source');
+    if (hasPlatformSource) {
+      this.db.run('CREATE INDEX IF NOT EXISTS idx_sdk_sessions_platform_source ON sdk_sessions(platform_source)');
+      this.db.run('CREATE UNIQUE INDEX IF NOT EXISTS ux_sdk_sessions_platform_content ON sdk_sessions(platform_source, content_session_id)');
+    }
+
     this.db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)').run(4, new Date().toISOString());
   }
 

tests/install-non-tty.test.ts

@@ -147,6 +147,18 @@ describe('Install Non-TTY Support', () => {
       expect(installSource).toContain('installCodexCli(marketplaceDirectory())');
     });
 
+    it('writes the install marker into the durable marketplace plugin root for Codex hook launches', () => {
+      expect(installSource).toContain('writeInstallMarker(marketplaceDirectory(), version, bunVersion, uvVersion)');
+    });
+
+    it('repairs the durable marketplace plugin root marker as well as the cache copy', () => {
+      const repairRegion = installSource.slice(
+        installSource.indexOf('export async function runRepairCommand'),
+        installSource.indexOf('if (isInteractive) {\n    p.outro'),
+      );
+      expect(repairRegion).toContain('writeInstallMarker(marketplaceDirectory(), version, bunVersion, uvVersion)');
+    });
+
     it('refreshes Codex marketplace cache after registration', () => {
       const installRegion = codexInstallerSource.slice(
         codexInstallerSource.indexOf('export async function installCodexCli'),

tests/setup-runtime.test.ts

@@ -72,6 +72,24 @@ describe('setup-runtime install marker', () => {
       const marker = readInstallMarker(tempDir);
       expect(marker).toEqual({ version: '12.4.4' });
     });
+
+    it('reads the marker from plugin/.install-version when given a marketplace root', () => {
+      mkdirSync(join(tempDir, 'plugin'), { recursive: true });
+      writeFileSync(join(tempDir, 'plugin', 'package.json'), JSON.stringify({ name: 'claude-mem' }));
+      writeFileSync(
+        join(tempDir, 'plugin', '.install-version'),
+        JSON.stringify({ version: '13.9.2', bun: '1.3.11', uv: '0.11.14', installedAt: '2026-07-01T00:00:00.000Z' }),
+      );
+
+      const marker = readInstallMarker(tempDir);
+
+      expect(marker).toEqual({
+        version: '13.9.2',
+        bun: '1.3.11',
+        uv: '0.11.14',
+        installedAt: '2026-07-01T00:00:00.000Z',
+      });
+    });
   });
 
   describe('writeInstallMarker', () => {
@@ -94,6 +112,16 @@ describe('setup-runtime install marker', () => {
       const parsed = JSON.parse(readFileSync(join(tempDir, '.install-version'), 'utf-8'));
       expect(Object.keys(parsed).sort()).toEqual(['bun', 'installedAt', 'uv', 'version'].sort());
     });
+
+    it('writes the marker into plugin/.install-version when targetDir is a marketplace root', () => {
+      mkdirSync(join(tempDir, 'plugin'), { recursive: true });
+      writeFileSync(join(tempDir, 'plugin', 'package.json'), JSON.stringify({ name: 'claude-mem' }));
+
+      writeInstallMarker(tempDir, '13.9.2', '1.3.11', '0.11.14');
+
+      expect(existsSync(join(tempDir, 'plugin', '.install-version'))).toBe(true);
+      expect(existsSync(join(tempDir, '.install-version'))).toBe(false);
+    });
   });
 
   describe('isInstallCurrent', () => {

tests/sqlite/session-store-migrations.test.ts

@@ -248,6 +248,132 @@ function seedLegacyGlobalContentIdentityScenario(db: Database): void {
   `).run(101, 'shared-raw-id', 'tool-1', epoch + 4);
 }
 
+function seedPrePlatformSourceSdkSessionsScenario(db: Database): void {
+  const now = new Date().toISOString();
+  const epoch = Date.now();
+
+  db.run(`
+    CREATE TABLE schema_versions (
+      id INTEGER PRIMARY KEY,
+      version INTEGER UNIQUE NOT NULL,
+      applied_at TEXT NOT NULL
+    )
+  `);
+
+  db.run(`
+    CREATE TABLE sdk_sessions (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      content_session_id TEXT UNIQUE NOT NULL,
+      memory_session_id TEXT UNIQUE,
+      project TEXT NOT NULL,
+      user_prompt TEXT,
+      started_at TEXT NOT NULL,
+      started_at_epoch INTEGER NOT NULL,
+      completed_at TEXT,
+      completed_at_epoch INTEGER,
+      status TEXT CHECK(status IN ('active', 'completed', 'failed')) NOT NULL DEFAULT 'active',
+      worker_port INTEGER,
+      prompt_counter INTEGER DEFAULT 0,
+      custom_title TEXT
+    )
+  `);
+
+  db.run(`
+    CREATE TABLE observations (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      memory_session_id TEXT NOT NULL,
+      project TEXT NOT NULL,
+      text TEXT,
+      type TEXT NOT NULL,
+      title TEXT,
+      subtitle TEXT,
+      facts TEXT,
+      narrative TEXT,
+      concepts TEXT,
+      files_read TEXT,
+      files_modified TEXT,
+      prompt_number INTEGER,
+      discovery_tokens INTEGER DEFAULT 0,
+      content_hash TEXT,
+      agent_type TEXT,
+      agent_id TEXT,
+      merged_into_project TEXT,
+      generated_by_model TEXT,
+      metadata TEXT,
+      created_at TEXT NOT NULL,
+      created_at_epoch INTEGER NOT NULL,
+      FOREIGN KEY(memory_session_id) REFERENCES sdk_sessions(memory_session_id) ON DELETE CASCADE ON UPDATE CASCADE
+    )
+  `);
+
+  db.run(`
+    CREATE TABLE session_summaries (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      memory_session_id TEXT NOT NULL,
+      project TEXT NOT NULL,
+      request TEXT,
+      investigated TEXT,
+      learned TEXT,
+      completed TEXT,
+      next_steps TEXT,
+      files_read TEXT,
+      files_edited TEXT,
+      notes TEXT,
+      prompt_number INTEGER,
+      discovery_tokens INTEGER DEFAULT 0,
+      merged_into_project TEXT,
+      created_at TEXT NOT NULL,
+      created_at_epoch INTEGER NOT NULL,
+      FOREIGN KEY(memory_session_id) REFERENCES sdk_sessions(memory_session_id) ON DELETE CASCADE ON UPDATE CASCADE
+    )
+  `);
+
+  db.run(`
+    CREATE TABLE user_prompts (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      content_session_id TEXT NOT NULL,
+      prompt_number INTEGER NOT NULL,
+      prompt_text TEXT NOT NULL,
+      created_at TEXT NOT NULL,
+      created_at_epoch INTEGER NOT NULL,
+      FOREIGN KEY(content_session_id) REFERENCES sdk_sessions(content_session_id) ON DELETE CASCADE
+    )
+  `);
+
+  db.run(`
+    CREATE TABLE pending_messages (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      session_db_id INTEGER NOT NULL,
+      content_session_id TEXT NOT NULL,
+      tool_use_id TEXT,
+      message_type TEXT NOT NULL CHECK(message_type IN ('observation', 'summarize')),
+      tool_name TEXT,
+      tool_input TEXT,
+      tool_response TEXT,
+      cwd TEXT,
+      last_user_message TEXT,
+      last_assistant_message TEXT,
+      prompt_number INTEGER,
+      status TEXT NOT NULL DEFAULT 'pending' CHECK(status IN ('pending', 'processing')),
+      created_at_epoch INTEGER NOT NULL,
+      agent_type TEXT,
+      agent_id TEXT,
+      FOREIGN KEY (session_db_id) REFERENCES sdk_sessions(id) ON DELETE CASCADE
+    )
+  `);
+
+  for (let version = 4; version <= 23; version++) {
+    db.prepare('INSERT INTO schema_versions (version, applied_at) VALUES (?, ?)').run(version, now);
+  }
+
+  db.prepare(`
+    INSERT INTO sdk_sessions (
+      content_session_id, memory_session_id, project, user_prompt,
+      started_at, started_at_epoch, status, worker_port, prompt_counter, custom_title
+    ) VALUES (?, ?, ?, ?, ?, ?, 'active', ?, ?, ?)
+  `).run('legacy-content-id', 'legacy-memory-id', 'legacy-project', 'legacy prompt', now, epoch, 37777, 1, 'Legacy Title');
+}
+
 describe('SessionStore migrations', () => {
   let store: SessionStore | undefined;
 
@@ -395,6 +521,39 @@ describe('SessionStore migrations', () => {
     }
   });
 
+  it('bootstraps a pre-platform_source sdk_sessions table without crashing initializeSchema', () => {
+    const db = new Database(':memory:');
+    try {
+      seedPrePlatformSourceSdkSessionsScenario(db);
+
+      expect(() => new SessionStore(db)).not.toThrow();
+
+      const cols = new Set((db.query('PRAGMA table_info(sdk_sessions)').all() as Array<{ name: string }>).map(c => c.name));
+      expect(cols.has('platform_source')).toBe(true);
+      expect(hasUniqueIndexOnColumns(db, 'sdk_sessions', ['platform_source', 'content_session_id'])).toBe(true);
+
+      const row = db.prepare(`
+        SELECT content_session_id, memory_session_id, project, platform_source, worker_port, prompt_counter, custom_title
+        FROM sdk_sessions
+        WHERE content_session_id = 'legacy-content-id'
+      `).get() as {
+        content_session_id: string;
+        memory_session_id: string;
+        project: string;
+        platform_source: string;
+        worker_port: number;
+        prompt_counter: number;
+        custom_title: string | null;
+      };
+      expect(row.platform_source).toBe('claude');
+      expect(row.worker_port).toBe(37777);
+      expect(row.prompt_counter).toBe(1);
+      expect(row.custom_title).toBe('Legacy Title');
+    } finally {
+      db.close();
+    }
+  });
+
   it('drops the dead pending_messages columns (retry_count / failed_at_epoch / completed_at_epoch / worker_pid) on a legacy db', () => {
     const db = new Database(':memory:');
     try {