Migration from Docker to Standalone Python Server (#73)

* Migration from docker to standalone server
Migration handling
Fixed tests
Use simpler in-memory storage
Support for concurrent logging to disk
Simplified direct connections to localhost

* Migration from docker / redis to standalone script
Updated tests
Updated run script
Fixed requirements
Use dotenv
Ask if user would like to install MCP in Claude Desktop once
Updated docs

* More cleanup and references to docker removed

* Cleanup

* Comments

* Fixed tests

* Fix GitHub Actions workflow for standalone Python architecture

- Install requirements-dev.txt for pytest and testing dependencies
- Remove Docker setup from simulation tests (now standalone)
- Simplify linting job to use requirements-dev.txt
- Update simulation tests to run directly without Docker

Fixes unit test failures in CI due to missing pytest dependency.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Remove simulation tests from GitHub Actions

- Removed simulation-tests job that makes real API calls
- Keep only unit tests (mocked, no API costs) and linting
- Simulation tests should be run manually with real API keys
- Reduces CI costs and complexity

GitHub Actions now only runs:
- Unit tests (569 tests, all mocked)
- Code quality checks (ruff, black)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Fixed tests

* Fixed tests

---------

Co-authored-by: Claude <noreply@anthropic.com>

docs/troubleshooting.md

@@ -24,7 +24,7 @@ claude.exe --debug
 
 Look for error messages in the console output, especially:
 - API key errors
-- Docker connection issues
+- Python/environment issues
 - File permission errors
 
 ### 3. Verify API Keys
@@ -40,60 +40,72 @@ cat .env
 # OPENAI_API_KEY=your-key-here
 ```
 
-If you need to update your API keys, edit the `.env` file and then run:
+If you need to update your API keys, edit the `.env` file and then restart Claude for changes to take effect.
+
+### 4. Check Server Logs
+
+View the server logs for detailed error information:
 
 ```bash
-# Restart services
-./run-server.sh
+# View recent logs
+tail -n 100 logs/mcp_server.log
 
-# Or restart and follow logs for troubleshooting
-./run-server.sh -f
-```
-
-This will validate your configuration and restart the services.
-
-### 4. Check Docker Logs
-
-View the container logs for detailed error information:
-
-```bash
-# Check if containers are running
-docker-compose ps
-
-# View MCP server logs (recommended - shows actual tool execution)
-docker exec zen-mcp-server tail -f -n 500 /tmp/mcp_server.log
+# Follow logs in real-time
+tail -f logs/mcp_server.log
 
 # Or use the -f flag when starting to automatically follow logs
 ./run-server.sh -f
-```
 
-**Note**: Due to MCP protocol limitations, `docker-compose logs` only shows startup logs, not tool execution logs. Always use the docker exec command above or the `-f` flag for debugging.
+# Search for errors
+grep "ERROR" logs/mcp_server.log
+```
 
 See [Logging Documentation](logging.md) for more details on accessing logs.
 
 ### 5. Common Issues
 
 **"Connection failed" in Claude Desktop**
-- Ensure Docker is running: `docker ps`
-- Restart services: `docker-compose restart`
+- Ensure the server path is correct in your Claude config
+- Run `./run-server.sh` to verify setup and see configuration
+- Check that Python is installed: `python3 --version`
 
 **"API key environment variable is required"**
 - Add your API key to the `.env` file
-- Run: `./run-server.sh` to validate and restart
+- Restart Claude Desktop after updating `.env`
 
 **File path errors**
 - Always use absolute paths: `/Users/you/project/file.py`
 - Never use relative paths: `./file.py`
 
-### 6. Still Having Issues?
+**Python module not found**
+- Run `./run-server.sh` to reinstall dependencies
+- Check virtual environment is activated: should see `.zen_venv` in the Python path
+
+### 6. Environment Issues
+
+**Virtual Environment Problems**
+```bash
+# Reset environment completely
+rm -rf .zen_venv
+./run-server.sh
+```
+
+**Permission Issues**
+```bash
+# Ensure script is executable
+chmod +x run-server.sh
+```
+
+### 7. Still Having Issues?
 
 If the problem persists after trying these steps:
 
 1. **Reproduce the issue** - Note the exact steps that cause the problem
-2. **Collect logs** - Save relevant error messages from Claude debug mode and Docker logs
+2. **Collect logs** - Save relevant error messages from Claude debug mode and server logs
 3. **Open a GitHub issue** with:
    - Your operating system
-   - Error messages
+   - Python version: `python3 --version`
+   - Error messages from logs
    - Steps to reproduce
    - What you've already tried