Add experimental Docker support and update configuration handling

- Introduced `DOCKER.md` with detailed setup instructions and limitations.
- Enhanced `compose.yaml` with dynamic port and environment variable support.
- Updated `agent.py` to detect Docker environments and disable GUI features.
- Modified configuration paths to support both Docker and non-Docker setups.
- Marked Docker support as experimental in the documentation.

DOCKER.md

@@ -0,0 +1,161 @@
+# Docker Setup for Serena (Experimental)
+
+⚠️ **EXPERIMENTAL FEATURE**: The Docker setup for Serena is currently experimental and has several limitations. Please read this entire document before using Docker with Serena.
+
+## Overview
+
+Docker support allows you to run Serena in an isolated container environment, which provides better security isolation for the shell tool and consistent dependencies across different systems.
+
+## Benefits
+
+- **Safer shell tool execution**: Commands run in an isolated container environment
+- **Consistent dependencies**: No need to manage language servers and dependencies on your host system
+- **Cross-platform support**: Works consistently across Windows, macOS, and Linux
+
+## Important Limitations and Caveats
+
+### 1. Configuration File Conflicts
+
+⚠️ **Critical**: Docker uses a separate configuration file (`serena_config.docker.yml`) to avoid path conflicts. When running in Docker:
+- Container paths will be stored in the configuration (e.g., `/workspaces/serena/...`)
+- These paths are incompatible with non-Docker usage
+- After using Docker, you cannot directly switch back to non-Docker usage without manual configuration adjustment
+
+### 2. Project Activation Limitations
+
+- **Only mounted directories work**: Projects must be mounted as volumes to be accessible
+- Projects outside the mounted directories cannot be activated or accessed
+- Default setup only mounts the current directory
+
+### 3. GUI Window Disabled
+
+- The GUI log window option is automatically disabled in Docker environments
+- Use the web dashboard instead (see below)
+
+### 4. Dashboard Port Configuration
+
+The web dashboard runs on port 24282 (0x5EDA) by default. You can configure this using environment variables:
+
+```bash
+# Use default ports
+docker-compose up serena
+
+# Use custom ports
+SERENA_DASHBOARD_PORT=8080 docker-compose up serena
+```
+
+⚠️ **Note**: If the local port is occupied, you'll need to specify a different port using the environment variable.
+
+### 5. Line Ending Issues on Windows
+
+⚠️ **Windows Users**: Be aware of potential line ending inconsistencies:
+- Files edited within the Docker container may use Unix line endings (LF)
+- Your Windows system may expect Windows line endings (CRLF)
+- This can cause issues with version control and text editors
+- Configure your Git settings appropriately: `git config core.autocrlf true`
+
+## Quick Start
+
+### Using Docker Compose (Recommended)
+
+1. **Production mode** (for using Serena as MCP server):
+   ```bash
+   docker-compose up serena
+   ```
+
+2. **Development mode** (with source code mounted):
+   ```bash
+   docker-compose up serena-dev
+   ```
+
+### Using Docker directly
+
+```bash
+# Build the image
+docker build -t serena .
+
+# Run with current directory mounted
+docker run -it --rm \
+  -v "$(pwd)":/workspace \
+  -p 9121:9121 \
+  -p 24282:24282 \
+  -e SERENA_DOCKER=1 \
+  serena
+```
+
+## Accessing the Dashboard
+
+Once running, access the web dashboard at:
+- Default: http://localhost:24282/dashboard
+- Custom port: http://localhost:${SERENA_DASHBOARD_PORT}/dashboard
+
+## Volume Mounting
+
+To work with projects, you must mount them as volumes:
+
+```yaml
+# In compose.yaml
+volumes:
+  - ./my-project:/workspace/my-project
+  - /path/to/another/project:/workspace/another-project
+```
+
+## Environment Variables
+
+- `SERENA_DOCKER=1`: Set automatically to indicate Docker environment
+- `SERENA_PORT`: MCP server port (default: 9121)
+- `SERENA_DASHBOARD_PORT`: Web dashboard port (default: 24282)
+
+## Troubleshooting
+
+### Port Already in Use
+
+If you see "port already in use" errors:
+```bash
+# Check what's using the port
+lsof -i :24282  # macOS/Linux
+netstat -ano | findstr :24282  # Windows
+
+# Use a different port
+SERENA_DASHBOARD_PORT=8080 docker-compose up serena
+```
+
+### Configuration Issues
+
+If you need to reset Docker configuration:
+```bash
+# Remove Docker-specific config
+rm serena_config.docker.yml
+
+# Serena will auto-generate a new one on next run
+```
+
+### Project Access Issues
+
+Ensure projects are properly mounted:
+- Check volume mounts in `docker-compose.yaml`
+- Use absolute paths for external projects
+- Verify permissions on mounted directories
+
+## Migration Path
+
+To switch between Docker and non-Docker usage:
+
+1. **Docker to Non-Docker**:
+   - Manually edit project paths in `serena_config.yml`
+   - Change container paths to host paths
+   - Or use separate config files for each environment
+
+2. **Non-Docker to Docker**:
+   - Projects will be re-registered with container paths
+   - Original config remains unchanged
+
+## Future Improvements
+
+We're working on:
+- Automatic config migration between environments
+- Better project path handling
+- Dynamic port allocation
+- Windows line-ending handling
+
+For updates and issues, please check the [GitHub repository](https://github.com/AbanteAI/serena).