feat: support multiple input formats for --docs argument

- Add support for multiple directories: --docs ./src ./tests ./config
- Add support for individual files: --docs ./file1.py ./file2.txt
- Add support for mixed files and directories: --docs ./README.md ./src/ ./config.json
- Add git ls-files integration: --docs $(git ls-files)
- Add git submodule detection and skip logic to avoid indexing third-party dependencies
- Add comprehensive error handling for path resolution issues
- Update MCP README with advanced usage examples including git integration
- Fix ruff linting issues with closure variable binding

Breaking changes: None - fully backward compatible with existing single directory usage

Examples:
  leann build my-repo --docs $(git ls-files) --embedding-mode sentence-transformers --embedding-model all-MiniLM-L6-v2 --backend hnsw
  leann build my-code --docs ./src ./tests ./docs --embedding-mode sentence-transformers --embedding-model all-MiniLM-L6-v2 --backend hnsw
  leann build my-configs --docs ./package.json ./tsconfig.json ./webpack.config.js --embedding-mode sentence-transformers --embedding-model all-MiniLM-L6-v2 --backend hnsw

README.md

@@ -468,7 +468,7 @@ leann --help
 ### Usage Examples
 
 ```bash
-# build from a specific directory, and my_docs is the index name
+# build from a specific directory, and my_docs is the index name(Here you can also build from multiple dict or multiple files)
 leann build my-docs --docs ./your_documents
 
 # Search your documents