feat: Fix observation timestamps, refactor session management, and enhance worker reliability (#437)

* Refactor worker version checks and increase timeout settings

- Updated the default hook timeout from 5000ms to 120000ms for improved stability.
- Modified the worker version check to log a warning instead of restarting the worker on version mismatch.
- Removed legacy PM2 cleanup and worker start logic, simplifying the ensureWorkerRunning function.
- Enhanced polling mechanism for worker readiness with increased retries and reduced interval.

* feat: implement worker queue polling to ensure processing completion before proceeding

* refactor: change worker command from start to restart in hooks configuration

* refactor: remove session management complexity

- Simplify createSDKSession to pure INSERT OR IGNORE
- Remove auto-create logic from storeObservation/storeSummary
- Delete 11 unused session management methods
- Derive prompt_number from user_prompts count
- Keep sdk_sessions table schema unchanged for compatibility

* refactor: simplify session management by removing unused methods and auto-creation logic

* Refactor session prompt number retrieval in SessionRoutes

- Updated the method of obtaining the prompt number from the session.
- Replaced `store.getPromptCounter(sessionDbId)` with `store.getPromptNumberFromUserPrompts(claudeSessionId)` for better clarity and accuracy.
- Adjusted the logic for incrementing the prompt number to derive it from the user prompts count instead of directly incrementing a counter.

* refactor: replace getPromptCounter with getPromptNumberFromUserPrompts in SessionManager

Phase 7 of session management simplification. Updates SessionManager to derive
prompt numbers from user_prompts table count instead of using the deprecated
prompt_counter column.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: simplify SessionCompletionHandler to use direct SQL query

Phase 8: Remove call to findActiveSDKSession() and replace with direct
database query in SessionCompletionHandler.completeByClaudeId().

This removes dependency on the deleted findActiveSDKSession() method
and simplifies the code by using a straightforward SELECT query.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: remove markSessionCompleted call from SDKAgent

- Delete call to markSessionCompleted() in SDKAgent.ts
- Session status is no longer tracked or updated
- Part of phase 9: simplifying session management

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: remove markSessionComplete method (Phase 10)

- Deleted markSessionComplete() method from DatabaseManager
- Removed markSessionComplete call from SessionCompletionHandler
- Session completion status no longer tracked in database
- Part of session management simplification effort

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* refactor: replace deleted updateSDKSessionId calls in import script (Phase 11)

- Replace updateSDKSessionId() calls with direct SQL UPDATE statements
- Method was deleted in Phase 3 as part of session management simplification
- Import script now uses direct database access consistently

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* test: add validation for SQL updates in sdk_sessions table

* refactor: enhance worker-cli to support manual and automated runs

* Remove cleanup hook and associated session completion logic

- Deleted the cleanup-hook implementation from the hooks directory.
- Removed the session completion endpoint that was used by the cleanup hook.
- Updated the SessionCompletionHandler to eliminate the completeByClaudeId method and its dependencies.
- Adjusted the SessionRoutes to reflect the removal of the session completion route.

* fix: update worker-cli command to use bun for consistency

* feat: Implement timestamp fix for observations and enhance processing logic

- Added `earliestPendingTimestamp` to `ActiveSession` to track the original timestamp of the earliest pending message.
- Updated `SDKAgent` to capture and utilize the earliest pending timestamp during response processing.
- Modified `SessionManager` to track the earliest timestamp when yielding messages.
- Created scripts for fixing corrupted timestamps, validating fixes, and investigating timestamp issues.
- Verified that all corrupted observations have been repaired and logic for future processing is sound.
- Ensured orphan processing can be safely re-enabled after validation.

* feat: Enhance SessionStore to support custom database paths and add timestamp fields for observations and summaries

* Refactor pending queue processing and add management endpoints

- Disabled automatic recovery of orphaned queues on startup; users must now use the new /api/pending-queue/process endpoint.
- Updated processOrphanedQueues method to processPendingQueues with improved session handling and return detailed results.
- Added new API endpoints for managing pending queues: GET /api/pending-queue and POST /api/pending-queue/process.
- Introduced a new script (check-pending-queue.ts) for checking and processing pending observation queues interactively or automatically.
- Enhanced logging and error handling for better monitoring of session processing.

* updated agent sdk

* feat: Add manual recovery guide and queue management endpoints to documentation

---------

Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>

src/services/worker/session/SessionCompletionHandler.ts

@@ -1,23 +1,20 @@
 /**
  * Session Completion Handler
  *
- * Consolidates session completion logic to eliminate duplication across
- * three different completion endpoints (DELETE, POST by DB ID, POST by Claude ID).
+ * Consolidates session completion logic for manual session deletion/completion.
+ * Used by DELETE /api/sessions/:id and POST /api/sessions/:id/complete endpoints.
  *
- * All completion flows follow the same pattern:
- * 1. Delete session from SessionManager (aborts SDK agent)
- * 2. Mark session complete in database
- * 3. Broadcast session completed event
+ * Completion flow:
+ * 1. Delete session from SessionManager (aborts SDK agent, cleans up in-memory state)
+ * 2. Broadcast session completed event (updates UI spinner)
  */
 
 import { SessionManager } from '../SessionManager.js';
-import { DatabaseManager } from '../DatabaseManager.js';
 import { SessionEventBroadcaster } from '../events/SessionEventBroadcaster.js';
 
 export class SessionCompletionHandler {
   constructor(
     private sessionManager: SessionManager,
-    private dbManager: DatabaseManager,
     private eventBroadcaster: SessionEventBroadcaster
   ) {}
 
@@ -29,34 +26,7 @@ export class SessionCompletionHandler {
     // Delete from session manager (aborts SDK agent)
     await this.sessionManager.deleteSession(sessionDbId);
 
-    // Mark session complete in database
-    this.dbManager.markSessionComplete(sessionDbId);
-
     // Broadcast session completed event
     this.eventBroadcaster.broadcastSessionCompleted(sessionDbId);
   }
-
-  /**
-   * Complete session by Claude session ID
-   * Used by POST /api/sessions/complete (cleanup-hook endpoint)
-   *
-   * @returns true if session was found and completed, false if no active session found
-   */
-  async completeByClaudeId(claudeSessionId: string): Promise<boolean> {
-    const store = this.dbManager.getSessionStore();
-
-    // Find session by claudeSessionId
-    const session = store.findActiveSDKSession(claudeSessionId);
-    if (!session) {
-      // No active session - nothing to clean up (may have already been completed)
-      return false;
-    }
-
-    const sessionDbId = session.id;
-
-    // Complete using standard flow
-    await this.completeByDbId(sessionDbId);
-
-    return true;
-  }
 }