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>

tests/test_directory_expansion_tracking.py

@@ -121,10 +121,10 @@ def helper_function():
             assert any(str(Path(f).resolve()) == expected_resolved for f in captured_files)
 
     @pytest.mark.asyncio
-    @patch("utils.conversation_memory.get_redis_client")
+    @patch("utils.conversation_memory.get_storage")
     @patch("providers.ModelProviderRegistry.get_provider_for_model")
     async def test_conversation_continuation_with_directory_files(
-        self, mock_get_provider, mock_redis, tool, temp_directory_with_files
+        self, mock_get_provider, mock_storage, tool, temp_directory_with_files
     ):
         """Test that conversation continuation works correctly with directory expansion"""
         # Setup mock Redis client with in-memory storage
@@ -140,7 +140,7 @@ def helper_function():
 
         mock_client.get.side_effect = mock_get
         mock_client.setex.side_effect = mock_setex
-        mock_redis.return_value = mock_client
+        mock_storage.return_value = mock_client
 
         # Setup mock provider
         mock_provider = create_mock_provider()
@@ -196,8 +196,8 @@ def helper_function():
         # This test shows the fix is working - conversation continuation properly filters out
         # already-embedded files. The exact length depends on whether any new files are found.
 
-    @patch("utils.conversation_memory.get_redis_client")
-    def test_get_conversation_embedded_files_with_expanded_files(self, mock_redis, tool, temp_directory_with_files):
+    @patch("utils.conversation_memory.get_storage")
+    def test_get_conversation_embedded_files_with_expanded_files(self, mock_storage, tool, temp_directory_with_files):
         """Test that get_conversation_embedded_files returns expanded files"""
         # Setup mock Redis client with in-memory storage
         mock_client = Mock()
@@ -212,7 +212,7 @@ def helper_function():
 
         mock_client.get.side_effect = mock_get
         mock_client.setex.side_effect = mock_setex
-        mock_redis.return_value = mock_client
+        mock_storage.return_value = mock_client
 
         directory = temp_directory_with_files["directory"]
         expected_files = temp_directory_with_files["files"]
@@ -237,8 +237,8 @@ def helper_function():
         assert set(embedded_files) == set(expected_files)
         assert directory not in embedded_files
 
-    @patch("utils.conversation_memory.get_redis_client")
-    def test_file_filtering_with_mixed_files_and_directories(self, mock_redis, tool, temp_directory_with_files):
+    @patch("utils.conversation_memory.get_storage")
+    def test_file_filtering_with_mixed_files_and_directories(self, mock_storage, tool, temp_directory_with_files):
         """Test file filtering when request contains both individual files and directories"""
         # Setup mock Redis client with in-memory storage
         mock_client = Mock()
@@ -253,7 +253,7 @@ def helper_function():
 
         mock_client.get.side_effect = mock_get
         mock_client.setex.side_effect = mock_setex
-        mock_redis.return_value = mock_client
+        mock_storage.return_value = mock_client
 
         directory = temp_directory_with_files["directory"]
         python_file = temp_directory_with_files["python_file"]