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/context-generator.ts

@@ -335,7 +335,7 @@ export async function generateContext(input?: ContextInput, useColors: boolean =
         priorAssistantMessage = messages.assistantMessage;
       }
     } catch (error) {
-      // Ignore
+      // Expected: Transcript file may not exist or be readable
     }
   }