feat: add full directory support and smart file handling

Major improvements to file handling capabilities:

- Add directory traversal support to all file-processing tools
- Tools now accept both individual files and entire directories
- Automatically expand directories and discover code files recursively
- Smart filtering: skip hidden files, __pycache__, and non-code files
- Progressive token loading: read as many files as possible within limits
- Clear file separation markers with full paths for Gemini

Key changes:
- Rewrite file_utils.py with expand_paths() and improved read_files()
- Update all tool descriptions to indicate directory support
- Add comprehensive tests for directory handling and token limits
- Document tool parameters and examples in README
- Bump version to 2.4.2

All tools (analyze, review_code, debug_issue, think_deeper) now support:
- Single files: "analyze main.py"
- Directories: "review src/"
- Mixed paths: "analyze config.py, src/, tests/"

This enables analyzing entire projects or specific subsystems efficiently
while respecting token limits and providing clear file boundaries.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

tools/think_deeper.py

@@ -27,7 +27,7 @@ class ThinkDeeperRequest(ToolRequest):
         description="Specific aspects to focus on (architecture, performance, security, etc.)",
     )
     reference_files: Optional[List[str]] = Field(
-        None, description="Optional file paths for additional context"
+        None, description="Optional file paths or directories for additional context"
     )