Refactor worker port handling and improve logging

- Replaced hardcoded migration port with dynamic port retrieval using `getWorkerPort()` in worker-cli.ts.
- Updated context generator to clarify error handling comments.
- Introduced timeout constants in ProcessManager for better maintainability.
- Configured SQLite settings using constants for mmap size and cache size in DatabaseManager.
- Added timeout constants for Git and NPM commands in BranchManager.
- Enhanced error logging in FormattingService and SearchManager to provide more context on failures.
- Removed deprecated silentDebug function and replaced its usage with logger.debug.
- Updated tests to use dynamic worker port retrieval instead of hardcoded values.

tests/happy-paths/session-init.test.ts

@@ -6,9 +6,10 @@
  */
 import { describe, it, expect, beforeEach, vi } from 'vitest';
 import { bashCommandScenario, sessionScenario } from '../helpers/scenarios.js';
+import { getWorkerPort } from '../../src/shared/worker-utils.js';
 
 describe('Session Initialization (UserPromptSubmit)', () => {
-  const WORKER_PORT = 37777;
+  const WORKER_PORT = getWorkerPort();
 
   beforeEach(() => {
     vi.clearAllMocks();