Format entire codebase with ruff and add type hints across all modules:
- Apply ruff formatting to all Python files (121 files, 17K insertions)
- Add type hints to function signatures throughout lightrag core and API
- Update test suite with improved type annotations and docstrings
- Add pyrightconfig.json for static type checking configuration
- Create prompt_optimized.py and test_extraction_prompt_ab.py test files
- Update ruff.toml and .gitignore for improved linting configuration
- Standardize code style across examples, reproduce scripts, and utilities
- Add entity_chunks & relation_chunks storage
- Implement KEEP/FIFO limit strategies
- Update env.example with new settings
- Add migration for chunk tracking data
- Support all KV storage
- Introduces an index mapping documents to their corresponding entities and relations. This significantly speeds up `adelete_by_doc_id` by replacing slow graph traversal with a fast key-value lookup.
- Refactors the ingestion pipeline (`merge_nodes_and_edges`) to populate this new index. Adds a one-time data migration script to backfill the index for existing data.
