diff --git a/tests/ra_aid/test_show_thoughts.py b/tests/ra_aid/test_show_thoughts.py
index 03ca51b..0f80465 100644
--- a/tests/ra_aid/test_show_thoughts.py
+++ b/tests/ra_aid/test_show_thoughts.py
@@ -17,67 +17,102 @@ def test_show_thoughts_flag():
     assert args.show_thoughts is True
 
 
-@pytest.fixture(autouse=True)
+@pytest.fixture
 def mock_config_repository():
     """Mock the ConfigRepository to avoid database operations during tests"""
-    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
-        # Setup a mock repository
-        mock_repo = MagicMock()
-        
-        # Create a dictionary to simulate config
-        config = {}
-        
-        # Setup get method to return config values
-        def get_config(key, default=None):
-            return config.get(key, default)
-        mock_repo.get.side_effect = get_config
-        
-        # Setup set method to update config values
-        def set_config(key, value):
-            config[key] = value
-        mock_repo.set.side_effect = set_config
-        
-        # Setup update method to update multiple config values
-        def update_config(config_dict):
-            config.update(config_dict)
-        mock_repo.update.side_effect = update_config
-        
-        # Setup get_all method to return the config dict
-        def get_all_config():
-            return config.copy()
-        mock_repo.get_all.side_effect = get_all_config
-        
-        # Make the mock context var return our mock repo
-        mock_repo_var.get.return_value = mock_repo
-        
-        yield mock_repo
+    mock_repo = MagicMock()
+    
+    # Create a dictionary to simulate config
+    config = {}
+    
+    # Setup get method to return config values
+    def get_config(key, default=None):
+        return config.get(key, default)
+    mock_repo.get.side_effect = get_config
+    
+    # Setup set method to update config values
+    def set_config(key, value):
+        config[key] = value
+    mock_repo.set.side_effect = set_config
+    
+    # Setup update method to update multiple config values
+    def update_config(config_dict):
+        config.update(config_dict)
+    mock_repo.update.side_effect = update_config
+    
+    # Setup get_all method to return the config dict
+    def get_all_config():
+        return config.copy()
+    mock_repo.get_all.side_effect = get_all_config
+    
+    return mock_repo
 
 
 def test_show_thoughts_config(mock_config_repository):
-    """Test that the show_thoughts flag is correctly stored in config."""
+    """Test that the --show-thoughts flag is correctly stored in config."""
     import sys
-    from unittest.mock import patch
     
-    from ra_aid.__main__ import main
+    # Create a mock parse_arguments function
+    def mock_parse_arguments(args=None):
+        # Create a mock arguments object with controlled values
+        mock_args = MagicMock()
+        mock_args.show_thoughts = "--show-thoughts" in sys.argv
+        # Explicitly set research_only and chat to False to avoid sys.exit(1)
+        mock_args.research_only = False
+        mock_args.chat = False
+        # Set message to a default value to avoid sys.exit(1) for missing message
+        mock_args.message = "test message"
+        mock_args.wipe_project_memory = False
+        mock_args.webui = False
+        return mock_args
     
-    # Reset mocks
+    # Test with --show-thoughts flag
+    with patch.object(sys, "argv", ["ra-aid", "--show-thoughts"]):
+        with patch("ra_aid.__main__.parse_arguments", side_effect=mock_parse_arguments):
+            # Mock ConfigRepositoryManager to return our mock
+            with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__',
+                       return_value=mock_config_repository):
+                # Mock the required dependencies to prevent actual execution
+                with patch("ra_aid.__main__.setup_logging"), \
+                     patch("ra_aid.__main__.DatabaseManager"), \
+                     patch("ra_aid.__main__.ensure_migrations_applied"), \
+                     patch("ra_aid.__main__.check_dependencies"), \
+                     patch("ra_aid.__main__.validate_environment", return_value=(True, [], True, [])), \
+                     patch("ra_aid.__main__.build_status"), \
+                     patch("ra_aid.__main__.console.print"), \
+                     patch("ra_aid.__main__.initialize_llm"), \
+                     patch("ra_aid.__main__.run_research_agent"):
+                    
+                    # Run the main function
+                    from ra_aid.__main__ import main
+                    main()
+                    
+                    # Verify that show_thoughts was set to True in config
+                    mock_config_repository.set.assert_any_call("show_thoughts", True)
+    
+    # Reset mock for second test
     mock_config_repository.set.reset_mock()
     
-    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
-    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
-        # Test with --show-thoughts flag
-        with patch.object(sys, "argv", ["ra-aid", "-m", "test message", "--show-thoughts"]):
-            with patch("ra_aid.__main__.run_research_agent", return_value=None):
-                main()
-                # Verify the show_thoughts flag is set to True in config
-                mock_config_repository.set.assert_any_call("show_thoughts", True)
-        
-        # Reset mocks
-        mock_config_repository.set.reset_mock()
-        
-        # Test without --show-thoughts flag (default: False)
-        with patch.object(sys, "argv", ["ra-aid", "-m", "test message"]):
-            with patch("ra_aid.__main__.run_research_agent", return_value=None):
-                main()
-                # Verify the show_thoughts flag is set to False in config
-                mock_config_repository.set.assert_any_call("show_thoughts", False)
\ No newline at end of file
+    # Test without --show-thoughts flag
+    with patch.object(sys, "argv", ["ra-aid"]):
+        with patch("ra_aid.__main__.parse_arguments", side_effect=mock_parse_arguments):
+            # Mock ConfigRepositoryManager to return our mock
+            with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__',
+                       return_value=mock_config_repository):
+                # Mock the required dependencies to prevent actual execution
+                with patch("ra_aid.__main__.setup_logging"), \
+                     patch("ra_aid.__main__.DatabaseManager"), \
+                     patch("ra_aid.__main__.ensure_migrations_applied"), \
+                     patch("ra_aid.__main__.check_dependencies"), \
+                     patch("ra_aid.__main__.validate_environment", return_value=(True, [], True, [])), \
+                     patch("ra_aid.__main__.build_status"), \
+                     patch("ra_aid.__main__.console.print"), \
+                     patch("ra_aid.__main__.initialize_llm"), \
+                     patch("ra_aid.__main__.run_research_agent"):
+                    
+                    # Run the main function
+                    from ra_aid.__main__ import main
+                    main()
+                    
+                    # Verify that show_thoughts was set to False in config
+                    mock_config_repository.set.assert_any_call("show_thoughts", False)
\ No newline at end of file