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>

examples/claude_config_docker_home.json

@@ -1,19 +0,0 @@
-{
-  "comment": "Docker configuration that mounts your home directory",
-  "comment2": "Update paths: /path/to/zen-mcp-server/.env and /Users/your-username",
-  "comment3": "The container auto-detects /workspace as sandbox from WORKSPACE_ROOT",
-  "mcpServers": {
-    "zen": {
-      "command": "docker",
-      "args": [
-        "run",
-        "--rm",
-        "-i",
-        "--env-file", "/path/to/zen-mcp-server/.env",
-        "-e", "WORKSPACE_ROOT=/Users/your-username",
-        "-v", "/Users/your-username:/workspace:ro",
-        "zen-mcp-server:latest"
-      ]
-    }
-  }
-}

examples/claude_config_macos.json

@@ -1,17 +1,11 @@
 {
-  "comment": "macOS configuration using Docker",
-  "comment2": "Ensure Docker is running and containers are started",
-  "comment3": "Run './run-server.sh' first to set up the environment",
+  "comment": "macOS configuration using standalone server",
+  "comment2": "Run './run-server.sh' to set up the environment and get exact paths",
+  "comment3": "Use './run-server.sh -c' to display the correct configuration",
   "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"]
     }
   }
-}
+}

examples/claude_config_wsl.json

@@ -1,18 +1,14 @@
 {
-  "comment": "Windows configuration using WSL with Docker",
-  "comment2": "Ensure Docker Desktop is running and WSL integration is enabled",
-  "comment3": "Run './run-server.sh' in WSL first to set up the environment",
+  "comment": "Windows configuration using WSL with standalone server",
+  "comment2": "Run './run-server.sh' in WSL to set up the environment and get exact paths",
+  "comment3": "Use './run-server.sh -c' to display the correct configuration",
   "mcpServers": {
     "zen": {
       "command": "wsl.exe",
       "args": [
-        "docker",
-        "exec",
-        "-i",
-        "zen-mcp-server",
-        "python",
-        "server.py"
+        "/path/to/zen-mcp-server/.zen_venv/bin/python",
+        "/path/to/zen-mcp-server/server.py"
       ]
     }
   }
-}
+}