refactor: consolidate update methods to use single ON CONFLICT approach

- Replace upsert_entity() with SQLite ON CONFLICT implementation
- Override update() to use atomic ON CONFLICT semantics
- Add update_by_file_path() convenience method
- Remove redundant *_optimistic method variants
- Update sync_service to use consolidated API

This simplifies the API while maintaining the same race condition
protection through SQLite's native conflict resolution.

Co-authored-by: Paul Hernandez <phernandez@users.noreply.github.com>

Author: github-actions[bot]