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/logging.md

@@ -11,49 +11,59 @@ The easiest way to monitor logs is to use the `-f` flag when starting the server
 
 This will start the server and immediately begin tailing the MCP server logs.
 
-## Viewing Logs in Docker
-
-To monitor MCP server activity in real-time:
-
-```bash
-# Follow MCP server logs (recommended)
-docker exec zen-mcp-server tail -f -n 500 /tmp/mcp_server.log
-
-# Or use the -f flag when starting the server
-./run-server.sh -f
-```
-
-**Note**: Due to MCP protocol limitations, container logs don't show tool execution details. Always use the commands above for debugging.
-
 ## Log Files
 
-Logs are stored in the container's `/tmp/` directory and rotate daily at midnight, keeping 7 days of history:
+Logs are stored in the `logs/` directory within your project folder:
 
-- **`mcp_server.log`** - Main server operations
-- **`mcp_activity.log`** - Tool calls and conversations
-- **`mcp_server_overflow.log`** - Overflow protection for large logs
+- **`mcp_server.log`** - Main server operations, API calls, and errors
+- **`mcp_activity.log`** - Tool calls and conversation tracking
 
-## Accessing Log Files
+Log files rotate automatically when they reach 20MB, keeping up to 10 rotated files.
 
-To access log files directly:
+## Viewing Logs
+
+To monitor MCP server activity:
 
 ```bash
-# Enter the container
-docker exec -it zen-mcp-server /bin/sh
+# Follow logs in real-time
+tail -f logs/mcp_server.log
 
-# View current logs
-cat /tmp/mcp_server.log
-cat /tmp/mcp_activity.log
+# View last 100 lines
+tail -n 100 logs/mcp_server.log
 
-# View previous days (with date suffix)
-cat /tmp/mcp_server.log.2024-06-14
+# View activity logs (tool calls only)
+tail -f logs/mcp_activity.log
+
+# Search for specific patterns
+grep "ERROR" logs/mcp_server.log
+grep "tool_name" logs/mcp_activity.log
 ```
 
 ## Log Level
 
-Set verbosity with `LOG_LEVEL` in your `.env` file or docker-compose.yml:
+Set verbosity with `LOG_LEVEL` in your `.env` file:
 
-```yaml
-environment:
-  - LOG_LEVEL=DEBUG  # Options: DEBUG, INFO, WARNING, ERROR
-```
+```env
+# Options: DEBUG, INFO, WARNING, ERROR
+LOG_LEVEL=INFO
+```
+
+- **DEBUG**: Detailed information for debugging
+- **INFO**: General operational messages (default)
+- **WARNING**: Warning messages
+- **ERROR**: Only error messages
+
+## Log Format
+
+Logs use a standardized format with timestamps:
+
+```
+2024-06-14 10:30:45,123 - module.name - INFO - Message here
+```
+
+## Tips
+
+- Use `./run-server.sh -f` for the easiest log monitoring experience
+- Activity logs show only tool-related events for cleaner output
+- Main server logs include all operational details
+- Logs persist across server restarts