Refactor: Enhance reliability, logging, and process management

[JacksonFergusonDev]

📝 Summary

This PR addresses several "silent failure" anti-patterns in the codebase. It introduces robust logging (full tracebacks), significantly improves the reliability of status checks using a PID file, and refactors the backup logic to be cleaner and safer.

🔍 Key Changes

1. Observability & Logging ("Errors should never pass silently")

• Fix Tracebacks: Replaced logger.error with logger.exception in the main daemon loop to capture full stack traces during crashes.
• Log Rotation: Increased RotatingFileHandler backup count from 1 to 5 to prevent history loss during crash loops.
• Centralization: Refactored logging initialization into a reusable setup_logging() function.

2. Configuration & Reliability

• PID File Management: Implemented a daemon.pid file to track the running process.
  • Before: show_status parsed launchctl/systemctl stdout (brittle).
  • After: show_status checks for the PID file and verifies the process is alive using os.kill(pid, 0).
• Config Hardening: Config.load now explicitly catches tomllib.TOMLDecodeError and fails fast with a helpful error message instead of silently loading defaults.

3. Code Structure

• Context Manager: Extracted the git index environment manipulation into a @temporary_index context manager.
  • Ensures pulsar_index is always cleaned up, even if the backup logic crashes.
  • Reduces indentation depth in run_backup.

4. Git Wrapper Improvements

• Exception Propagation: Modified get_last_commit_time to raise exceptions instead of returning "Never". This allows the CLI to distinguish between a "New Repository" and a "Broken Repository" (marked as ERROR in list_repos).

✅ Checklist

• Daemon writes PID file on startup and cleans up on exit.
• CLI accurately reports status using PID check.
• Malformed config files cause immediate exit (no silent defaults).
• Logs now contain stack traces for unhandled exceptions.