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/services/sqlite/Database.ts

@@ -1,6 +1,10 @@
 import { Database } from 'bun:sqlite';
 import { DATA_DIR, DB_PATH, ensureDir } from '../../shared/paths.js';
 
+// SQLite configuration constants
+const SQLITE_MMAP_SIZE_BYTES = 256 * 1024 * 1024; // 256MB
+const SQLITE_CACHE_SIZE_PAGES = 10_000;
+
 export interface Migration {
   version: number;
   up: (db: Database) => void;
@@ -51,8 +55,8 @@ export class DatabaseManager {
     this.db.run('PRAGMA synchronous = NORMAL');
     this.db.run('PRAGMA foreign_keys = ON');
     this.db.run('PRAGMA temp_store = memory');
-    this.db.run('PRAGMA mmap_size = 268435456'); // 256MB
-    this.db.run('PRAGMA cache_size = 10000');
+    this.db.run(`PRAGMA mmap_size = ${SQLITE_MMAP_SIZE_BYTES}`);
+    this.db.run(`PRAGMA cache_size = ${SQLITE_CACHE_SIZE_PAGES}`);
 
     // Initialize schema_versions table
     this.initializeSchemaVersions();