refactor: Consolidate tools and add tooling optimizer agent

- Moved debug_paths.py from src/markitect/tools/ to tools/ for centralized tool organization
- Added tooling-optimizer agent specification to replace agent_tooling_optimizer.py script
- Updated .gitignore to allow debug_paths.py as legitimate tool (not temporary debug file)
- Removed empty src/markitect/tools/ directory

Organization: All development tools now consolidated in tools/ directory
Agent: Converted standalone script to proper Claude Code agent specification
Tooling: Improved discoverability and maintenance of development utilities

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

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

.gitignore

@@ -83,8 +83,9 @@ markitect.db
 # Issue workspace (temporary development files)
 .markitect_workspace/
 
-# Debug and temporary files
+# Debug and temporary files (exclude debug_paths.py which is a legitimate tool)
 debug_*.py
+!tools/debug_paths.py
 
 # Claude Code local settings (user-specific permissions)
 .claude/settings.local.json