Critical Fixes:
- Fixed IOC extraction order: URLs now checked before domains to prevent duplicates
- Fixed overlapping IOC highlights with overlap detection
- Fixed IPv4 pattern to validate octets (0-255) preventing invalid IPs like 999.999.999.999
- Fixed IPv6 pattern to support compressed format (::)
- Fixed hash extraction order: SHA256 -> SHA1 -> MD5 to prevent misclassification
High Priority Fixes:
- Added 10s timeout to all GPG subprocess calls to prevent hangs
- Fixed indentation inconsistency in storage.py:253
Performance Improvements:
- Removed 8 time.sleep(0.1) calls from demo case creation (800ms faster startup)
Robustness Improvements:
- Added error handling to export_markdown() for IOError/OSError/PermissionError
- Implemented atomic writes for state file (set_active)
- Implemented atomic writes for settings file (set_setting)
All changes tested and verified with unit tests.
- Move all project files from `trace/` subdirectory to the repository root
- Rename directory structure from `fnote` to `trace`
- Update package references and imports (fnote -> trace)
- Update application branding and storage paths (~/.trace)
- Update build script and documentation
- Ensure __pycache__ is ignored
