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>

tests/validate_sql_update.test.ts

@@ -0,0 +1,54 @@
+import { Database } from 'bun:sqlite';
+import { describe, it, expect, beforeEach, afterEach } from 'bun:test';
+
+describe('Refactor Validation: SQL Updates', () => {
+  let db: Database;
+
+  beforeEach(() => {
+    db = new Database(':memory:');
+    // Minimal schema for sdk_sessions based on SessionStore.ts migration004
+    db.run(`
+      CREATE TABLE sdk_sessions (
+        id INTEGER PRIMARY KEY AUTOINCREMENT,
+        claude_session_id TEXT UNIQUE NOT NULL,
+        sdk_session_id TEXT UNIQUE,
+        project TEXT NOT NULL,
+        user_prompt TEXT,
+        started_at TEXT,
+        started_at_epoch INTEGER,
+        completed_at TEXT,
+        completed_at_epoch INTEGER,
+        status TEXT DEFAULT 'active'
+      );
+    `);
+  });
+
+  afterEach(() => {
+    db.close();
+  });
+
+  it('should update sdk_session_id using direct SQL (replacing updateSDKSessionId)', () => {
+    // Setup initial state: A session without an sdk_session_id
+    const claudeId = 'claude-session-123';
+    const syntheticId = 'sdk-session-456';
+    
+    db.prepare(`
+      INSERT INTO sdk_sessions (claude_session_id, project, started_at, started_at_epoch)
+      VALUES (?, ?, ?, ?)
+    `).run(claudeId, 'test-project', '2025-01-01T00:00:00Z', 1735689600000);
+
+    // Verify initial state
+    const before = db.prepare('SELECT sdk_session_id FROM sdk_sessions WHERE claude_session_id = ?').get(claudeId) as any;
+    expect(before.sdk_session_id).toBeNull();
+
+    // EXECUTE: The exact SQL statement from the refactor in import-xml-observations.ts
+    // Original code: db['db'].prepare('UPDATE sdk_sessions SET sdk_session_id = ? WHERE claude_session_id = ?').run(syntheticSdkSessionId, sessionMeta.sessionId);
+    
+    const stmt = db.prepare('UPDATE sdk_sessions SET sdk_session_id = ? WHERE claude_session_id = ?');
+    stmt.run(syntheticId, claudeId);
+
+    // VERIFY: The update happened
+    const after = db.prepare('SELECT sdk_session_id FROM sdk_sessions WHERE claude_session_id = ?').get(claudeId) as any;
+    expect(after.sdk_session_id).toBe(syntheticId);
+  });
+});