Fix directory expansion tracking in conversation memory

When directories were provided to tools, only the directory path was stored
in conversation history instead of the individual expanded files. This caused
file filtering to incorrectly skip files in continued conversations.

Changes:
- Modified _prepare_file_content_for_prompt to return (content, processed_files)
- Updated all tools to track actually processed files for conversation memory
- Ensures directories are tracked as their expanded individual files

Fixes issue where Swift directory with 46 files was not properly embedded
in conversation continuations.

tools/thinkdeep.py

@@ -148,7 +148,8 @@ class ThinkDeepTool(BaseTool):
         if request.files:
             # Use centralized file processing logic
             continuation_id = getattr(request, "continuation_id", None)
-            file_content = 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:
                 context_parts.append(f"\n=== REFERENCE FILES ===\n{file_content}\n=== END FILES ===")