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/tools/debug.md

@@ -79,7 +79,7 @@ bug hunting and reduces the chance of wasting precious tokens back and forth.
 
 **Runtime Environment Issues:**
 ```
-"Debug deployment issues with Docker container startup failures, here's the runtime info: [environment details]"
+"Debug deployment issues with server startup failures, here's the runtime info: [environment details]"
 ```
 
 ## Debugging Methodology

docs/tools/listmodels.md

@@ -56,7 +56,7 @@ The tool displays:
 
 🔹 Custom/Local - ✅ Configured
   • local-llama (llama3.2) - 128K context, local inference
-  • Available at: http://host.docker.internal:11434/v1
+  • Available at: http://localhost:11434/v1
 
 🔹 OpenRouter - ❌ Not configured
   Set OPENROUTER_API_KEY to enable access to Claude, GPT-4, and more models

docs/tools/version.md

@@ -42,8 +42,8 @@ The tool provides:
 **System Information:**
 - Server uptime and status
 - Memory and resource usage (if available)
-- Connection status with Redis (for conversation memory)
-- Docker container information
+- Conversation memory status
+- Server process information
 
 ## Example Output
 
@@ -58,7 +58,7 @@ The tool provides:
 ⚙️ Configuration:
 • Default Model: auto
 • Providers: Google ✅, OpenAI ✅, Custom ✅
-• Conversation Memory: Redis ✅
+• Conversation Memory: Active ✅
 • Web Search: Enabled
 
 🛠️ Available Tools (12):
@@ -77,8 +77,8 @@ The tool provides:
 
 🔍 System Status:
 • Server Uptime: 2h 35m
-• Redis Connection: Active
-• Docker Container: zen-mcp-server (running)
+• Memory Storage: Active
+• Server Process: Running
 ```
 
 ## When to Use Version Tool
@@ -106,7 +106,7 @@ The version tool can help diagnose common issues:
 **Performance Troubleshooting:**
 - Server uptime and stability
 - Resource usage patterns
-- Redis connection health
+- Memory storage health
 
 ## Tool Parameters