- Update import paths from `freeflowuniverse.herolib` to `incubaid.herolib`
- Ensure `ws.parent.save()` is only called when `ws.parent` is present
- Remove redundant symlink cleanup for `freeflowuniverse.herolib`
- Refactor Directory struct and its methods.
- Update file selection logic for directories and files.
- Enhance prompt generation with better file mapping.
- Add unit tests for directory and file operations.
- Improve workspace management with auto-save and logging.