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.

src/utils/silent-debug.ts

@@ -83,12 +83,7 @@ export function clearSilentLog(): void {
   try {
     appendFileSync(LOG_FILE, `\n${'='.repeat(80)}\n[${new Date().toISOString()}] Log cleared\n${'='.repeat(80)}\n\n`);
   } catch (error) {
-    // Ignore errors
+    // Expected: Log file may not be writable
   }
 }
 
-/**
- * @deprecated Use happy_path_error__with_fallback instead
- * Backward compatibility alias for silentDebug
- */
-export const silentDebug = happy_path_error__with_fallback;