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/refactor.py

@@ -330,13 +330,14 @@ class RefactorTool(BaseTool):
         # Use standard file content preparation with dynamic token budget and line numbers
         try:
             logger.debug(f"[REFACTOR] Preparing file content for {len(examples_to_process)} style examples")
-            content = self._prepare_file_content_for_prompt(
+            content, processed_files = self._prepare_file_content_for_prompt(
                 examples_to_process,
                 continuation_id,
                 "Style guide examples",
                 max_tokens=style_examples_budget,
                 reserve_tokens=1000,
             )
+            # Store processed files for tracking - style examples are tracked separately from main code files
 
             # Determine how many files were actually included
             if content:
@@ -478,9 +479,10 @@ class RefactorTool(BaseTool):
 
         # Use centralized file processing logic for main code files (with line numbers enabled)
         logger.debug(f"[REFACTOR] Preparing {len(code_files_to_process)} code files for analysis")
-        code_content = self._prepare_file_content_for_prompt(
+        code_content, processed_files = self._prepare_file_content_for_prompt(
             code_files_to_process, continuation_id, "Code to analyze", max_tokens=remaining_tokens, reserve_tokens=2000
         )
+        self._actually_processed_files = processed_files
 
         if code_content:
             from utils.token_utils import estimate_tokens