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>

simulator_tests/test_content_validation.py

@@ -22,42 +22,6 @@ class ContentValidationTest(BaseSimulatorTest):
     def test_description(self) -> str:
         return "Content validation and duplicate detection"
 
-    def get_docker_logs_since(self, since_time: str) -> str:
-        """Get docker logs since a specific timestamp"""
-        try:
-            # Check both main server and log monitor for comprehensive logs
-            cmd_server = ["docker", "logs", "--since", since_time, self.container_name]
-            cmd_monitor = ["docker", "logs", "--since", since_time, "zen-mcp-log-monitor"]
-
-            import subprocess
-
-            result_server = subprocess.run(cmd_server, capture_output=True, text=True)
-            result_monitor = subprocess.run(cmd_monitor, capture_output=True, text=True)
-
-            # Get the internal log files which have more detailed logging
-            server_log_result = subprocess.run(
-                ["docker", "exec", self.container_name, "cat", "/tmp/mcp_server.log"], capture_output=True, text=True
-            )
-
-            activity_log_result = subprocess.run(
-                ["docker", "exec", self.container_name, "cat", "/tmp/mcp_activity.log"], capture_output=True, text=True
-            )
-
-            # Combine all logs
-            combined_logs = (
-                result_server.stdout
-                + "\n"
-                + result_monitor.stdout
-                + "\n"
-                + server_log_result.stdout
-                + "\n"
-                + activity_log_result.stdout
-            )
-            return combined_logs
-        except Exception as e:
-            self.logger.error(f"Failed to get docker logs: {e}")
-            return ""
-
     def run_test(self) -> bool:
         """Test that file processing system properly handles file deduplication"""
         try:
@@ -151,9 +115,9 @@ DATABASE_CONFIG = {
             else:
                 self.logger.warning("  ⚠️  Different tool failed")
 
-            # Validate file processing behavior from Docker logs
+            # Validate file processing behavior from server logs
             self.logger.info("  4: Validating file processing logs")
-            logs = self.get_docker_logs_since(start_time)
+            logs = self.get_server_logs_since(start_time)
 
             # Check for proper file embedding logs
             embedding_logs = [