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>

.env.example

@@ -1,11 +1,6 @@
 # Zen MCP Server Environment Configuration
 # Copy this file to .env and fill in your values
 
-# Required: Workspace root directory for file access
-# This should be the HOST path that contains all files Claude might reference
-# Defaults to $HOME for direct usage, auto-configured for Docker
-WORKSPACE_ROOT=/Users/your-username
-
 # API Keys - At least one is required
 #
 # IMPORTANT: Use EITHER OpenRouter OR native APIs (Gemini/OpenAI), not both!
@@ -27,10 +22,7 @@ XAI_API_KEY=your_xai_api_key_here
 OPENROUTER_API_KEY=your_openrouter_api_key_here
 
 # Option 3: Use custom API endpoints for local models (Ollama, vLLM, LM Studio, etc.)
-# IMPORTANT: Since this server ALWAYS runs in Docker, you MUST use host.docker.internal instead of localhost
-# ❌ WRONG: http://localhost:11434/v1 (Docker containers cannot reach localhost)
-# ✅ CORRECT: http://host.docker.internal:11434/v1 (Docker can reach host services)
-# CUSTOM_API_URL=http://host.docker.internal:11434/v1  # Ollama example (NOT localhost!)
+# CUSTOM_API_URL=http://localhost:11434/v1  # Ollama example
 # CUSTOM_API_KEY=                                      # Empty for Ollama (no auth needed)
 # CUSTOM_MODEL_NAME=llama3.2                          # Default model name
 
@@ -95,9 +87,7 @@ DEFAULT_THINKING_MODE_THINKDEEP=high
 # Override the default location of custom_models.json
 # CUSTOM_MODELS_CONFIG_PATH=/path/to/your/custom_models.json
 
-# Optional: Redis configuration (auto-configured for Docker)
-# The Redis URL for conversation threading - typically managed by docker-compose
-# REDIS_URL=redis://redis:6379/0
+# Note: Redis is no longer used - conversations are stored in memory
 
 # Optional: Conversation timeout (hours)
 # How long AI-to-AI conversation threads persist before expiring