refactor(core): unify repository registry management and atomic file operations

[JacksonFergusonDev]

Summary

This PR consolidates repository registry file operations and concurrency locking into a centralized, thread-safe, and process-safe API in system.py:

1. Centralized Registry Management API:

   • Enhanced get_registered_repos(registry_path: Path | None = None) -> list[Path] to evaluate the registry path dynamically and safely handle non-existent files.
   • Added add_repo_to_registry(repo_path: Path | str, registry_path: Path | None = None) -> bool for atomic path registration with fcntl.LOCK_EX and duplicate prevention.
   • Added remove_repo_from_registry(repo_path: Path | str, registry_path: Path | None = None) -> bool for atomic path removal with fcntl.LOCK_EX, .tmp swap, and os.fsync.
   • Added write_registered_repos(repos: Sequence[Path | str], registry_path: Path | None = None) -> bool for atomic full-registry overwrites (used by doctor cleanup).

2. Refactored Callers:

   • daemon.prune_registry: Simplified from ~40 lines of manual locking/swapping to a concise call to system.remove_repo_from_registry.
   • cli.setup_repo: Simplified registration logic using system.add_repo_to_registry.
   • cli.unregister_repo: Simplified removal logic using system.remove_repo_from_registry.
   • cli.doctor and cli.diagnostics: Replaced raw file reads and writes with system.write_registered_repos and system.get_registered_repos.
   • Removed duplicate import fcntl from daemon.py and cli.py.

3. Automated Tests:

   • Added unit tests in tests/test_system.py covering path addition, deduplication, removal, atomic writing, and OSError resilience.
   • Verified property-based tests in tests/test_properties.py.

Verification

• All 166 pytest tests passing locally.
• Pre-commit hooks (ruff check, ruff format, mypy) passing cleanly.