refactor: Convert main() coroutine to Click CLI group for extensible subcommands

cli/CLI_COMMANDS.md

@@ -0,0 +1,137 @@
+# DeepCode CLI Commands
+
+## Overview
+
+The DeepCode CLI has been restructured using Click to support multiple subcommands. This allows for better organization and extensibility.
+
+## Available Commands
+
+### Main Command Group
+
+```bash
+python cli/cli_app.py --help
+```
+
+Shows all available commands and options.
+
+### Run Interactive Session (Default)
+
+```bash
+# All of these are equivalent:
+python cli/cli_app.py
+python cli/cli_app.py run
+```
+
+Launches the interactive DeepCode CLI session where you can:
+- Process research papers from URLs
+- Upload and process local files
+- Chat with the AI to generate code
+- View processing history
+- Configure settings
+
+### Configuration Management
+
+```bash
+python cli/cli_app.py config
+```
+
+Shows configuration options (placeholder for future implementation).
+
+**Planned features:**
+- View current configuration
+- Set default processing mode (comprehensive/optimized)
+- Configure API keys and endpoints
+- Manage workspace settings
+
+### Cleanup Utility
+
+```bash
+# Clean Python cache files
+python cli/cli_app.py clean --cache
+
+# Clean log files
+python cli/cli_app.py clean --logs
+
+# Clean everything
+python cli/cli_app.py clean --all
+```
+
+Removes temporary files and caches to free up disk space.
+
+## Adding New Subcommands
+
+To add a new subcommand, simply add a new function decorated with `@cli.command()` in `cli/cli_app.py`:
+
+```python
+@cli.command()
+@click.option('--option-name', help='Description')
+def my_command(option_name):
+    """Description of what this command does"""
+    # Your implementation here
+    click.echo("Command executed!")
+```
+
+## Examples
+
+### Basic Usage
+
+```bash
+# Start interactive session
+python cli/cli_app.py
+
+# Or explicitly use the run command
+python cli/cli_app.py run
+```
+
+### Cleanup Examples
+
+```bash
+# Clean only cache files
+python cli/cli_app.py clean --cache
+
+# Clean only logs
+python cli/cli_app.py clean --logs
+
+# Clean everything
+python cli/cli_app.py clean --all
+```
+
+### Getting Help
+
+```bash
+# General help
+python cli/cli_app.py --help
+
+# Help for specific command
+python cli/cli_app.py clean --help
+python cli/cli_app.py config --help
+```
+
+## Version Information
+
+```bash
+python cli/cli_app.py --version
+```
+
+## Migration Notes
+
+### For Developers
+
+The previous `main()` coroutine has been renamed to `run_interactive_cli()` and is now wrapped by Click commands:
+
+- **Old:** `asyncio.run(main())`
+- **New:** `cli()` (Click group) → `run()` command → `run_interactive_cli()`
+
+### Backward Compatibility
+
+The CLI launcher (`cli_launcher.py`) has been updated to use the new Click-based structure, maintaining backward compatibility with existing workflows.
+
+## Future Enhancements
+
+Potential subcommands to add:
+- `deepcode process --file <path>` - Direct file processing
+- `deepcode process --url <url>` - Direct URL processing
+- `deepcode history` - View processing history
+- `deepcode export` - Export results
+- `deepcode doctor` - Check system dependencies and configuration
+

cli/__init__.py

@@ -11,8 +11,8 @@
 __version__ = "1.0.0"
 __author__ = "DeepCode Team - Data Intelligence Lab @ HKU"
 
-from .cli_app import main as cli_main
+from .cli_app import cli, run_interactive_cli
 from .cli_interface import CLIInterface
 from .cli_launcher import main as launcher_main
 
-__all__ = ["cli_main", "CLIInterface", "launcher_main"]
+__all__ = ["cli", "run_interactive_cli", "CLIInterface", "launcher_main"]