diff --git a/config.py b/config.py
index d3bcd8f..c626bc7 100644
--- a/config.py
+++ b/config.py
@@ -14,7 +14,7 @@ import os
 # These values are used in server responses and for tracking releases
 # IMPORTANT: This is the single source of truth for version and author info
 # Semantic versioning: MAJOR.MINOR.PATCH
-__version__ = "4.6.0"
+__version__ = "4.6.1"
 # Last update date in ISO format
 __updated__ = "2025-06-15"
 # Primary maintainer
diff --git a/tests/test_auto_mode.py b/tests/test_auto_mode.py
index 3a2be41..aeb6346 100644
--- a/tests/test_auto_mode.py
+++ b/tests/test_auto_mode.py
@@ -150,21 +150,40 @@ class TestAutoMode:
 
             tool = AnalyzeTool()
 
-            # Mock the provider to simulate o3 not being available
-            with patch("providers.registry.ModelProviderRegistry.get_provider_for_model") as mock_provider:
-                # Mock that o3 is not available but flash/pro are
+            # Get currently available models to use in the test
+            from providers.registry import ModelProviderRegistry
+
+            available_models = ModelProviderRegistry.get_available_model_names()
+
+            # Mock the provider to simulate o3 not being available but keep actual available models
+            with (
+                patch("providers.registry.ModelProviderRegistry.get_provider_for_model") as mock_provider,
+                patch("providers.registry.ModelProviderRegistry.get_available_models") as mock_available,
+                patch.object(tool, "_get_available_models") as mock_tool_available,
+            ):
+
+                # Mock that o3 is not available but actual available models are
                 def mock_get_provider(model_name):
-                    if model_name in ["flash", "pro", "gemini-2.5-flash-preview-05-20", "gemini-2.5-pro-preview-06-05"]:
-                        # Return a mock provider for available models
+                    if model_name == "o3":
+                        # o3 is specifically not available
+                        return None
+                    elif model_name in available_models:
+                        # Return a mock provider for actually available models
                         from unittest.mock import MagicMock
 
                         return MagicMock()
                     else:
-                        # o3 and others are not available
+                        # Other unknown models are not available
                         return None
 
                 mock_provider.side_effect = mock_get_provider
 
+                # Mock available models to return the actual available models
+                mock_available.return_value = dict.fromkeys(available_models, "test")
+
+                # Mock the tool's available models method to return the actual available models
+                mock_tool_available.return_value = available_models
+
                 # Execute with unavailable model
                 result = await tool.execute(
                     {"files": ["/tmp/test.py"], "prompt": "Analyze this", "model": "o3"}  # This model is not available
@@ -176,8 +195,10 @@ class TestAutoMode:
             assert "error" in response
             assert "Model 'o3' is not available" in response
             assert "Available models:" in response
-            # Should list the available models
-            assert "flash" in response or "pro" in response
+
+            # Should list at least one of the actually available models
+            has_available_model = any(model in response for model in available_models)
+            assert has_available_model, f"Expected one of {available_models} to be in response: {response}"
 
         finally:
             # Restore
diff --git a/tests/test_directory_expansion_tracking.py b/tests/test_directory_expansion_tracking.py
new file mode 100644
index 0000000..b9da217
--- /dev/null
+++ b/tests/test_directory_expansion_tracking.py
@@ -0,0 +1,322 @@
+"""
+Test for directory expansion tracking in conversation memory
+
+This test ensures that when directories are provided to tools, the individual
+expanded files are properly tracked in conversation history rather than just
+the directory paths. This prevents file filtering bugs in conversation
+continuations.
+"""
+
+from pathlib import Path
+from unittest.mock import Mock, patch
+
+import pytest
+
+from tests.mock_helpers import create_mock_provider
+from tools.chat import ChatTool
+from tools.models import ToolOutput
+from utils.conversation_memory import add_turn, create_thread
+
+
+class TestDirectoryExpansionTracking:
+    """Test directory expansion tracking in conversation memory"""
+
+    @pytest.fixture
+    def tool(self):
+        return ChatTool()
+
+    @pytest.fixture
+    def temp_directory_with_files(self, project_path):
+        """Create a temporary directory with multiple files"""
+        # Create within the project path to avoid security restrictions
+        temp_dir = project_path / "test_temp_dir"
+        temp_dir.mkdir(exist_ok=True)
+        temp_path = temp_dir
+
+        # Create multiple Swift files (simulating the original bug scenario)
+        files = []
+        for i in range(5):
+            swift_file = temp_path / f"File{i}.swift"
+            swift_file.write_text(
+                f"""
+import Foundation
+
+class TestClass{i} {{
+    func testMethod{i}() -> String {{
+        return "test{i}"
+    }}
+}}
+"""
+            )
+            files.append(str(swift_file))
+
+        # Create a Python file as well
+        python_file = temp_path / "helper.py"
+        python_file.write_text(
+            """
+def helper_function():
+    return "helper"
+"""
+        )
+        files.append(str(python_file))
+
+        try:
+            yield {
+                "directory": str(temp_dir),
+                "files": files,
+                "swift_files": files[:-1],  # All but the Python file
+                "python_file": str(python_file),
+            }
+        finally:
+            # Cleanup
+            import shutil
+
+            shutil.rmtree(temp_dir, ignore_errors=True)
+
+    @pytest.mark.asyncio
+    @patch("providers.ModelProviderRegistry.get_provider_for_model")
+    async def test_directory_expansion_tracked_in_conversation_memory(
+        self, mock_get_provider, tool, temp_directory_with_files
+    ):
+        """Test that directory expansion is properly tracked in conversation memory"""
+        # Setup mock provider
+        mock_provider = create_mock_provider()
+        mock_get_provider.return_value = mock_provider
+
+        directory = temp_directory_with_files["directory"]
+        expected_files = temp_directory_with_files["files"]
+
+        # Create a request with the directory (not individual files)
+        request_args = {
+            "prompt": "Analyze this codebase structure",
+            "files": [directory],  # Directory path, not individual files
+            "model": "flash",
+        }
+
+        # Execute the tool
+        result = await tool.execute(request_args)
+
+        # Verify the tool executed successfully
+        assert result is not None
+        result_data = result[0].text
+        tool_output = ToolOutput.model_validate_json(result_data)
+        assert tool_output.status in ["success", "continuation_available"]
+
+        # Verify that the actually processed files were the expanded individual files
+        captured_files = getattr(tool, "_actually_processed_files", [])
+        assert captured_files is not None
+        assert len(captured_files) == len(expected_files)
+
+        # Convert to sets for comparison (order might differ)
+        # Normalize paths to handle /private prefix differences
+        captured_set = {str(Path(f).resolve()) for f in captured_files}
+        expected_set = {str(Path(f).resolve()) for f in expected_files}
+        assert captured_set == expected_set
+
+        # Verify that the directory was expanded to individual files
+        assert directory not in captured_files  # Directory itself should not be in the list
+        for expected_file in expected_files:
+            # Normalize path for comparison
+            expected_resolved = str(Path(expected_file).resolve())
+            assert any(str(Path(f).resolve()) == expected_resolved for f in captured_files)
+
+    @pytest.mark.asyncio
+    @patch("utils.conversation_memory.get_redis_client")
+    @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
+    ):
+        """Test that conversation continuation works correctly with directory expansion"""
+        # Setup mock Redis client with in-memory storage
+        mock_client = Mock()
+        redis_storage = {}  # Simulate Redis storage
+
+        def mock_get(key):
+            return redis_storage.get(key)
+
+        def mock_setex(key, ttl, value):
+            redis_storage[key] = value
+            return True
+
+        mock_client.get.side_effect = mock_get
+        mock_client.setex.side_effect = mock_setex
+        mock_redis.return_value = mock_client
+
+        # Setup mock provider
+        mock_provider = create_mock_provider()
+        mock_get_provider.return_value = mock_provider
+
+        directory = temp_directory_with_files["directory"]
+        expected_files = temp_directory_with_files["files"]
+
+        # Step 1: Create a conversation thread manually with the expanded files
+        thread_id = create_thread("chat", {"prompt": "Initial analysis", "files": [directory]})
+
+        # Add a turn with the expanded files (simulating what the fix should do)
+        success = add_turn(
+            thread_id,
+            "assistant",
+            "I've analyzed the codebase structure.",
+            files=expected_files,  # Individual expanded files, not directory
+            tool_name="chat",
+        )
+        assert success is True
+
+        # Step 2: Continue the conversation with the same directory
+        continuation_args = {
+            "prompt": "Now focus on the Swift files specifically",
+            "files": [directory],  # Same directory again
+            "model": "flash",
+            "continuation_id": thread_id,
+        }
+
+        # Mock to capture file filtering behavior
+        original_filter_new_files = tool.filter_new_files
+        filtered_files = None
+
+        def capture_filtering_mock(requested_files, continuation_id):
+            nonlocal filtered_files
+            filtered_files = original_filter_new_files(requested_files, continuation_id)
+            return filtered_files
+
+        with patch.object(tool, "filter_new_files", side_effect=capture_filtering_mock):
+            # Execute continuation - this should not re-embed the same files
+            result = await tool.execute(continuation_args)
+
+        # Verify the tool executed successfully
+        assert result is not None
+        result_data = result[0].text
+        tool_output = ToolOutput.model_validate_json(result_data)
+        assert tool_output.status in ["success", "continuation_available"]
+
+        # Verify that file filtering worked correctly
+        # The directory might still be included if it contains files not yet embedded,
+        # but the key point is that we don't re-embed already processed individual files
+        assert filtered_files is not None
+        # 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):
+        """Test that get_conversation_embedded_files returns expanded files"""
+        # Setup mock Redis client with in-memory storage
+        mock_client = Mock()
+        redis_storage = {}  # Simulate Redis storage
+
+        def mock_get(key):
+            return redis_storage.get(key)
+
+        def mock_setex(key, ttl, value):
+            redis_storage[key] = value
+            return True
+
+        mock_client.get.side_effect = mock_get
+        mock_client.setex.side_effect = mock_setex
+        mock_redis.return_value = mock_client
+
+        directory = temp_directory_with_files["directory"]
+        expected_files = temp_directory_with_files["files"]
+
+        # Create a thread with expanded files
+        thread_id = create_thread("chat", {"prompt": "Initial analysis", "files": [directory]})
+
+        # Add a turn with expanded files
+        success = add_turn(
+            thread_id,
+            "assistant",
+            "Analysis complete.",
+            files=expected_files,  # Individual files
+            tool_name="chat",
+        )
+        assert success is True
+
+        # Get the embedded files from conversation
+        embedded_files = tool.get_conversation_embedded_files(thread_id)
+
+        # Verify that we get the individual files, not the directory
+        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):
+        """Test file filtering when request contains both individual files and directories"""
+        # Setup mock Redis client with in-memory storage
+        mock_client = Mock()
+        redis_storage = {}  # Simulate Redis storage
+
+        def mock_get(key):
+            return redis_storage.get(key)
+
+        def mock_setex(key, ttl, value):
+            redis_storage[key] = value
+            return True
+
+        mock_client.get.side_effect = mock_get
+        mock_client.setex.side_effect = mock_setex
+        mock_redis.return_value = mock_client
+
+        directory = temp_directory_with_files["directory"]
+        python_file = temp_directory_with_files["python_file"]
+
+        # Create a thread with some expanded files
+        thread_id = create_thread("chat", {"prompt": "Initial analysis", "files": [directory]})
+
+        # Add a turn with only some of the files (simulate partial embedding)
+        swift_files = temp_directory_with_files["swift_files"]
+        success = add_turn(
+            thread_id,
+            "assistant",
+            "Swift analysis complete.",
+            files=swift_files,  # Only Swift files
+            tool_name="chat",
+        )
+        assert success is True
+
+        # Request with both directory and individual file
+        mixed_request = [directory, python_file]
+        filtered_files = tool.filter_new_files(mixed_request, thread_id)
+
+        # The directory should expand to individual files, and since Swift files
+        # are already embedded, only the python file should be new
+        # Note: the filter_new_files method handles directory expansion internally
+        assert python_file in filtered_files
+        # The directory itself might be in the filtered list if it expands to new files
+        # In this case, since we only embedded Swift files, the directory might still be included
+
+    @pytest.mark.asyncio
+    @patch("providers.ModelProviderRegistry.get_provider_for_model")
+    async def test_actually_processed_files_stored_correctly(self, mock_get_provider, tool, temp_directory_with_files):
+        """Test that _actually_processed_files is stored correctly after file processing"""
+        # Setup mock provider
+        mock_provider = create_mock_provider()
+        mock_get_provider.return_value = mock_provider
+
+        directory = temp_directory_with_files["directory"]
+        expected_files = temp_directory_with_files["files"]
+
+        # Execute the tool
+        request_args = {
+            "prompt": "Analyze this code",
+            "files": [directory],
+            "model": "flash",
+        }
+
+        result = await tool.execute(request_args)
+
+        # Verify the tool executed successfully
+        assert result is not None
+
+        # Verify that _actually_processed_files was set correctly
+        assert hasattr(tool, "_actually_processed_files")
+        actually_processed = tool._actually_processed_files
+
+        # Should contain individual files, not the directory
+        # Normalize paths to handle /private prefix differences
+        processed_set = {str(Path(f).resolve()) for f in actually_processed}
+        expected_set = {str(Path(f).resolve()) for f in expected_files}
+        assert processed_set == expected_set
+        assert directory not in actually_processed
+
+
+if __name__ == "__main__":
+    pytest.main([__file__])
diff --git a/tests/test_large_prompt_handling.py b/tests/test_large_prompt_handling.py
index f0c4482..a8b5bb8 100644
--- a/tests/test_large_prompt_handling.py
+++ b/tests/test_large_prompt_handling.py
@@ -224,7 +224,7 @@ class TestLargePromptHandling:
 
             # Mock the centralized file preparation method to avoid file system access
             with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare_files:
-                mock_prepare_files.return_value = "File content"
+                mock_prepare_files.return_value = ("File content", [other_file])
 
                 await tool.execute({"prompt": "", "files": [temp_prompt_file, other_file]})
 
diff --git a/tests/test_per_tool_model_defaults.py b/tests/test_per_tool_model_defaults.py
index 896509d..a46cc4d 100644
--- a/tests/test_per_tool_model_defaults.py
+++ b/tests/test_per_tool_model_defaults.py
@@ -292,7 +292,7 @@ class TestFileContentPreparation:
             tool._current_model_name = "auto"
 
             # Call the method
-            tool._prepare_file_content_for_prompt(["/test/file.py"], None, "test")
+            content, processed_files = tool._prepare_file_content_for_prompt(["/test/file.py"], None, "test")
 
             # Check that it logged the correct message
             debug_calls = [call for call in mock_logger.debug.call_args_list if "Auto mode detected" in str(call)]
diff --git a/tests/test_precommit.py b/tests/test_precommit.py
index 8f65d41..4d764b6 100644
--- a/tests/test_precommit.py
+++ b/tests/test_precommit.py
@@ -256,7 +256,10 @@ class TestPrecommitTool:
 
         # Mock the centralized file preparation method
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare_files:
-            mock_prepare_files.return_value = "=== FILE: config.py ===\nCONFIG_VALUE = 42\n=== END FILE ==="
+            mock_prepare_files.return_value = (
+                "=== FILE: config.py ===\nCONFIG_VALUE = 42\n=== END FILE ===",
+                ["/test/path/config.py"],
+            )
 
             request = PrecommitRequest(
                 path="/absolute/repo/path",
@@ -320,7 +323,7 @@ class TestPrecommitTool:
 
         # Mock the centralized file preparation method to return empty (file not found)
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare_files:
-            mock_prepare_files.return_value = ""
+            mock_prepare_files.return_value = ("", [])
             result_with_files = await tool.prepare_prompt(request_with_files)
 
         assert "If you need additional context files" not in result_with_files
diff --git a/tests/test_precommit_with_mock_store.py b/tests/test_precommit_with_mock_store.py
index 026aee3..4cd8b28 100644
--- a/tests/test_precommit_with_mock_store.py
+++ b/tests/test_precommit_with_mock_store.py
@@ -232,7 +232,7 @@ TEMPERATURE_ANALYTICAL = 0.2  # For code review, debugging
         temp_dir, config_path = temp_repo
 
         # Test the centralized file preparation method directly
-        file_content = tool._prepare_file_content_for_prompt(
+        file_content, processed_files = tool._prepare_file_content_for_prompt(
             [config_path],
             None,
             "Test files",
diff --git a/tests/test_prompt_regression.py b/tests/test_prompt_regression.py
index 1b3ea9f..5ad91cd 100644
--- a/tests/test_prompt_regression.py
+++ b/tests/test_prompt_regression.py
@@ -75,7 +75,7 @@ class TestPromptRegression:
 
             # Mock file reading through the centralized method
             with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare_files:
-                mock_prepare_files.return_value = "File content here"
+                mock_prepare_files.return_value = ("File content here", ["/path/to/file.py"])
 
                 result = await tool.execute({"prompt": "Analyze this code", "files": ["/path/to/file.py"]})
 
diff --git a/tests/test_refactor.py b/tests/test_refactor.py
index faad4b2..541c82d 100644
--- a/tests/test_refactor.py
+++ b/tests/test_refactor.py
@@ -143,7 +143,7 @@ class TestRefactorTool:
 
             # Mock file processing
             with patch.object(refactor_tool, "_prepare_file_content_for_prompt") as mock_prepare:
-                mock_prepare.return_value = "def test(): pass"
+                mock_prepare.return_value = ("def test(): pass", ["/test/file.py"])
 
                 result = await refactor_tool.execute(
                     {
@@ -172,7 +172,7 @@ class TestRefactorTool:
 
             # Mock file processing
             with patch.object(refactor_tool, "_prepare_file_content_for_prompt") as mock_prepare:
-                mock_prepare.return_value = "def example(): pass"
+                mock_prepare.return_value = ("def example(): pass", ["/test/file.py"])
 
             with patch.object(refactor_tool, "_process_style_guide_examples") as mock_style:
                 mock_style.return_value = ("# style guide content", "")
diff --git a/tests/test_testgen.py b/tests/test_testgen.py
index d0ab3bf..3c19426 100644
--- a/tests/test_testgen.py
+++ b/tests/test_testgen.py
@@ -205,7 +205,10 @@ class TestComprehensive(unittest.TestCase):
             mock_filter.return_value = [temp_files["small_test"], temp_files["large_test"]]
 
             with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-                mock_prepare.return_value = "Mocked test content"
+                mock_prepare.return_value = (
+                    "Mocked test content",
+                    [temp_files["small_test"], temp_files["large_test"]],
+                )
 
                 # Test with available tokens
                 content, note = tool._process_test_examples(
@@ -224,7 +227,7 @@ class TestComprehensive(unittest.TestCase):
             mock_filter.return_value = [temp_files["large_test"], temp_files["small_test"]]
 
             with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-                mock_prepare.return_value = "test content"
+                mock_prepare.return_value = ("test content", [temp_files["small_test"], temp_files["large_test"]])
 
                 tool._process_test_examples(
                     [temp_files["large_test"], temp_files["small_test"]], None, available_tokens=50000
@@ -244,7 +247,7 @@ class TestComprehensive(unittest.TestCase):
         request = TestGenRequest(files=[temp_files["code_file"]], prompt="Test the calculator functions")
 
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-            mock_prepare.return_value = "mocked file content"
+            mock_prepare.return_value = ("mocked file content", [temp_files["code_file"]])
 
             prompt = await tool.prepare_prompt(request)
 
@@ -263,7 +266,7 @@ class TestComprehensive(unittest.TestCase):
         )
 
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-            mock_prepare.return_value = "mocked content"
+            mock_prepare.return_value = ("mocked content", [temp_files["code_file"]])
 
             with patch.object(tool, "_process_test_examples") as mock_process:
                 mock_process.return_value = ("test examples content", "Note: examples included")
@@ -328,7 +331,7 @@ class TestComprehensive(unittest.TestCase):
                 mock_process.return_value = ("test content", "")
 
                 with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-                    mock_prepare.return_value = "code content"
+                    mock_prepare.return_value = ("code content", ["/tmp/test.py"])
 
                     request = TestGenRequest(
                         files=["/tmp/test.py"], prompt="Test prompt", test_examples=["/tmp/example.py"]
@@ -348,7 +351,7 @@ class TestComprehensive(unittest.TestCase):
     async def test_continuation_support(self, tool, temp_files):
         """Test continuation ID support"""
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-            mock_prepare.return_value = "code content"
+            mock_prepare.return_value = ("code content", [temp_files["code_file"]])
 
             request = TestGenRequest(
                 files=[temp_files["code_file"]], prompt="Continue testing", continuation_id="test-thread-123"
@@ -372,7 +375,7 @@ class TestComprehensive(unittest.TestCase):
         request = TestGenRequest(files=[temp_files["code_file"]], prompt="Generate tests")
 
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-            mock_prepare.return_value = "code content"
+            mock_prepare.return_value = ("code content", [temp_files["code_file"]])
 
             import asyncio
 
@@ -399,7 +402,7 @@ class TestComprehensive(unittest.TestCase):
 
         def capture_prepare_calls(files, *args, **kwargs):
             captured_calls.append(("prepare", files))
-            return "mocked content"
+            return ("mocked content", files)
 
         with patch.object(tool, "_prepare_file_content_for_prompt", side_effect=capture_prepare_calls):
             await tool.prepare_prompt(request)
@@ -427,7 +430,7 @@ class TestComprehensive(unittest.TestCase):
         )
 
         with patch.object(tool, "_prepare_file_content_for_prompt") as mock_prepare:
-            mock_prepare.return_value = "mocked content"
+            mock_prepare.return_value = ("mocked content", [temp_files["code_file"], temp_files["large_test"]])
 
             await tool.prepare_prompt(request)
 
@@ -461,7 +464,7 @@ class TestComprehensive(unittest.TestCase):
 
         def capture_prepare_calls(files, *args, **kwargs):
             captured_calls.append(("prepare", files))
-            return "mocked content"
+            return ("mocked content", files)
 
         with patch.object(tool, "_prepare_file_content_for_prompt", side_effect=capture_prepare_calls):
             await tool.prepare_prompt(request)
diff --git a/tools/base.py b/tools/base.py
index 6cb612f..021dd3d 100644
--- a/tools/base.py
+++ b/tools/base.py
@@ -719,9 +719,12 @@ class BaseTool(ABC):
             try:
                 # Before calling read_files, expand directories to get individual file paths
                 from utils.file_utils import expand_paths
+
                 expanded_files = expand_paths(files_to_embed)
-                logger.debug(f"[FILES] {self.name}: Expanded {len(files_to_embed)} paths to {len(expanded_files)} individual files")
-                
+                logger.debug(
+                    f"[FILES] {self.name}: Expanded {len(files_to_embed)} paths to {len(expanded_files)} individual files"
+                )
+
                 file_content = read_files(
                     files_to_embed,
                     max_tokens=effective_max_tokens + reserve_tokens,
@@ -730,7 +733,7 @@ class BaseTool(ABC):
                 )
                 self._validate_token_limit(file_content, context_description)
                 content_parts.append(file_content)
-                
+
                 # Track the expanded files as actually processed
                 actually_processed_files.extend(expanded_files)
 
@@ -742,7 +745,9 @@ class BaseTool(ABC):
                     f"{self.name} tool successfully embedded {len(files_to_embed)} files ({content_tokens:,} tokens)"
                 )
                 logger.debug(f"[FILES] {self.name}: Successfully embedded files - {content_tokens:,} tokens used")
-                logger.debug(f"[FILES] {self.name}: Actually processed {len(actually_processed_files)} individual files")
+                logger.debug(
+                    f"[FILES] {self.name}: Actually processed {len(actually_processed_files)} individual files"
+                )
             except Exception as e:
                 logger.error(f"{self.name} tool failed to embed files {files_to_embed}: {type(e).__name__}: {e}")
                 logger.debug(f"[FILES] {self.name}: File embedding failed - {type(e).__name__}: {e}")
@@ -772,7 +777,9 @@ class BaseTool(ABC):
                 logger.debug(f"[FILES] {self.name}: No skipped files to note")
 
         result = "".join(content_parts) if content_parts else ""
-        logger.debug(f"[FILES] {self.name}: _prepare_file_content_for_prompt returning {len(result)} chars, {len(actually_processed_files)} processed files")
+        logger.debug(
+            f"[FILES] {self.name}: _prepare_file_content_for_prompt returning {len(result)} chars, {len(actually_processed_files)} processed files"
+        )
         return result, actually_processed_files
 
     def get_websearch_instruction(self, use_websearch: bool, tool_specific: Optional[str] = None) -> str:
diff --git a/tools/debug.py b/tools/debug.py
index 83274ee..bd7cb39 100644
--- a/tools/debug.py
+++ b/tools/debug.py
@@ -166,7 +166,9 @@ class DebugIssueTool(BaseTool):
         if request.files:
             # Use centralized file processing logic
             continuation_id = getattr(request, "continuation_id", None)
-            file_content, processed_files = self._prepare_file_content_for_prompt(request.files, continuation_id, "Code")
+            file_content, processed_files = self._prepare_file_content_for_prompt(
+                request.files, continuation_id, "Code"
+            )
             self._actually_processed_files = processed_files
 
             if file_content:
diff --git a/tools/thinkdeep.py b/tools/thinkdeep.py
index 20f3533..efbe7d8 100644
--- a/tools/thinkdeep.py
+++ b/tools/thinkdeep.py
@@ -148,7 +148,9 @@ class ThinkDeepTool(BaseTool):
         if request.files:
             # Use centralized file processing logic
             continuation_id = getattr(request, "continuation_id", None)
-            file_content, processed_files = self._prepare_file_content_for_prompt(request.files, continuation_id, "Reference files")
+            file_content, processed_files = self._prepare_file_content_for_prompt(
+                request.files, continuation_id, "Reference files"
+            )
             self._actually_processed_files = processed_files
 
             if file_content: