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>

claude_config_example.json

@@ -1,17 +1,11 @@
 {
   "comment": "Example Claude Desktop configuration for Zen MCP Server",
-  "comment2": "For Docker setup, use examples/claude_config_docker_home.json",
+  "comment2": "Run './run-server.sh -c' to get the exact configuration for your system",
   "comment3": "For platform-specific examples, see the examples/ directory",
   "mcpServers": {
     "zen": {
-      "command": "docker",
-      "args": [
-        "exec",
-        "-i",
-        "zen-mcp-server",
-        "python",
-        "server.py"
-      ]
+      "command": "/path/to/zen-mcp-server/.zen_venv/bin/python",
+      "args": ["/path/to/zen-mcp-server/server.py"]
     }
   }
 }