fix: improve FilePersistenceService code quality and security

CRITICAL fixes:
- Add SemaphoreSlim for thread-safe file operations
- Add Console.WriteLine error logging for diagnostics
- Implement atomic file writes using temp file + File.Replace

MAJOR fixes:
- Add instanceId validation to prevent path traversal attacks
- Make JsonSerializerOptions static readonly for thread safety
- Add error handling in constructor for Directory.CreateDirectory

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>