update readme

Author: anhnh2002

.DS_Store

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+# Development Guide
+
+This guide provides information for developers who want to contribute to or extend CodeWiki.
+
+## Project Structure
+
+```
+codewiki/
+├── codewiki/                 # Main package
+│   ├── cli/                  # CLI implementation
+│   │   ├── commands/         # CLI commands (config, generate)
+│   │   ├── models/           # Data models
+│   │   ├── utils/            # Utilities
+│   │   └── adapters/         # External integrations
+│   ├── src/                  # Web application
+│   │   ├── be/               # Backend (dependency analysis, agents)
+│   │   │   ├── agent_orchestrator.py
+│   │   │   ├── agent_tools/
+│   │   │   ├── cluster_modules.py
+│   │   │   ├── dependency_analyzer/
+│   │   │   ├── documentation_generator.py
+│   │   │   └── llm_services.py
+│   │   └── fe/               # Frontend (web interface)
+│   │       ├── web_app.py
+│   │       ├── routes.py
+│   │       ├── github_processor.py
+│   │       └── visualise_docs.py
+│   ├── templates/            # HTML templates
+│   └── run_web_app.py        # Web app entry point
+├── docker/                   # Docker configuration
+│   ├── Dockerfile
+│   ├── docker-compose.yml
+│   └── env.example
+├── img/                      # Images and assets
+├── paper/                    # Research paper source
+├── tests/                    # Test suite
+├── output/                   # Generated documentation output
+├── pyproject.toml           # Project metadata
+├── requirements.txt         # Python dependencies
+└── README.md                # Main documentation
+```
+
+## Development Setup
+
+### Prerequisites
+
+- Python 3.12+
+- Node.js (for mermaid validation)
+- Git
+- Tree-sitter language parsers
+
+### Installation
+
+```bash
+# Clone the repository
+git clone https://github.com/FSoft-AI4Code/CodeWiki.git
+cd CodeWiki
+
+# Create virtual environment
+python3.12 -m venv .venv
+source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+
+# Install in development mode
+pip install -e .
+
+# Install development dependencies
+pip install -r requirements.txt
+```
+
+## Core Components
+
+### Backend Architecture
+
+#### 1. Dependency Analysis (`src/be/dependency_analyzer/`)
+
+- **AST Parser**: Tree-sitter based parsing for 7 languages
+- **Dependency Graph Builder**: Constructs call graphs and dependency relationships
+- **Analyzers**: Language-specific analyzers (Python, Java, JavaScript, TypeScript, C, C++, C#)
+
+#### 2. Module Clustering (`src/be/cluster_modules.py`)
+
+- Hierarchical decomposition of repository structure
+- Feature-oriented module partitioning
+- Topological sorting for dependency ordering
+
+#### 3. Agent System (`src/be/agent_orchestrator.py`)
+
+- Recursive agent-based documentation generation
+- Dynamic delegation for complex modules
+- Cross-module reference management
+
+#### 4. Agent Tools (`src/be/agent_tools/`)
+
+- `read_code_components.py`: Code reading utilities
+- `generate_sub_module_documentations.py`: Sub-module documentation generation
+- `str_replace_editor.py`: Documentation editing tools
+- `deps.py`: Dependency traversal tools
+
+### Frontend Architecture
+
+#### Web Application (`src/fe/`)
+
+- **FastAPI Backend**: `web_app.py`, `routes.py`
+- **GitHub Integration**: `github_processor.py`
+- **Documentation Viewer**: `visualise_docs.py`
+- **Background Processing**: `background_worker.py`
+
+### CLI Architecture
+
+#### Command Structure (`cli/commands/`)
+
+- `config.py`: Configuration management
+- `generate.py`: Documentation generation
+
+#### Utilities (`cli/utils/`)
+
+- `fs.py`: File system operations
+- `validation.py`: Input validation
+- `progress.py`: Progress tracking
+- `logging.py`: Logging configuration
+
+## Adding Support for New Languages
+
+To add support for a new programming language:
+
+1. **Add language analyzer** in `src/be/dependency_analyzer/analyzers/`:
+
+```python
+# new_language.py
+from .base import BaseAnalyzer
+
+class NewLanguageAnalyzer(BaseAnalyzer):
+    def __init__(self):
+        super().__init__("new_language")
+    
+    def extract_dependencies(self, ast_node):
+        # Implement dependency extraction
+        pass
+    
+    def extract_components(self, ast_node):
+        # Implement component extraction
+        pass
+```
+
+2. **Register the analyzer** in `src/be/dependency_analyzer/ast_parser.py`:
+
+```python
+LANGUAGE_ANALYZERS = {
+    # ... existing languages ...
+    "new_language": NewLanguageAnalyzer,
+}
+```
+
+3. **Add file extensions** in configuration
+
+4. **Add tests** for the new language
+
+## Testing
+
+```bash
+# Run all tests
+pytest
+
+# Run specific test file
+pytest tests/test_dependency_analyzer.py
+
+# Run with coverage
+pytest --cov=codewiki tests/
+```
+
+## Code Style
+
+- Follow PEP 8 for Python code
+- Use type hints where applicable
+- Write docstrings for public functions and classes
+- Keep functions focused and modular
+
+## Contributing
+
+1. **Fork the repository**
+2. **Create a feature branch**: `git checkout -b feature/your-feature`
+3. **Make your changes**
+4. **Write/update tests**
+5. **Ensure tests pass**: `pytest`
+6. **Commit your changes**: `git commit -am 'Add new feature'`
+7. **Push to the branch**: `git push origin feature/your-feature`
+8. **Submit a pull request**
+
+## Documentation Generation Workflow
+
+```mermaid
+graph TB
+    A[Repository Input] --> B[Dependency Graph Construction]
+    B --> C[Hierarchical Decomposition]
+    C --> D[Module Tree]
+    D --> E[Recursive Agent Processing]
+    E --> F{Complexity Check}
+    F -->|Complex| G[Dynamic Delegation]
+    F -->|Simple| H[Generate Documentation]
+    G --> E
+    H --> I[Cross-Module References]
+    I --> J[Hierarchical Assembly]
+    J --> K[Comprehensive Documentation]
+```
+
+## Debugging
+
+### Enable Verbose Logging
+
+```bash
+# CLI
+codewiki generate --verbose
+
+# Environment variable
+export CODEWIKI_LOG_LEVEL=DEBUG
+```
+
+### Common Issues
+
+**Tree-sitter parser errors**:
+- Ensure language parsers are properly installed
+- Check file encoding (UTF-8 expected)
+
+**LLM API errors**:
+- Verify API keys and endpoints
+- Check rate limits
+- Enable retry logic
+
+**Memory issues with large repositories**:
+- Adjust module decomposition threshold
+- Increase delegation depth limit
+
+## Performance Optimization
+
+- **Caching**: Results are cached to avoid redundant processing
+- **Parallel Processing**: Multiple modules can be processed concurrently
+- **Incremental Updates**: Only process changed modules (future work)
+
+## Support
+
+For development questions:
+- GitHub Issues: https://github.com/FSoft-AI4Code/CodeWiki/issues
+- Main Documentation: [README.md](README.md)
+