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>

tools/debug_paths.py

@@ -0,0 +1,51 @@
+import tempfile
+from pathlib import Path
+from click.testing import CliRunner
+from markitect.shared.cli import cli
+from markitect.ast_cache import ASTCache
+
+# Create test similar to failing test
+temp_dir = tempfile.mkdtemp()
+cache_dir = Path(temp_dir) / ".ast_cache"
+
+# Create test file
+test_file = Path(temp_dir) / "test.md"
+test_file.write_text("# Test")
+
+print(f"Temp dir: {temp_dir}")
+print(f"Cache dir: {cache_dir}")
+print(f"Test file: {test_file}")
+
+# Create cache like test does
+cache = ASTCache(cache_dir)
+cache.cache_file(test_file)
+
+# Check cache files exist
+cache_files = list(cache_dir.glob("*.ast.json"))
+print(f"Cache files created: {len(cache_files)}")
+print(f"Cache files: {cache_files}")
+
+# Now run CLI in temp dir context
+runner = CliRunner()
+
+# Test 1: In current working directory
+print("\n=== Test 1: Current working directory ===")
+result1 = runner.invoke(cli, ['cache-clean'])
+print(f"Exit code: {result1.exit_code}")
+print(f"Output: {repr(result1.output)}")
+
+# Test 2: Change working directory
+print(f"\n=== Test 2: Change to temp directory ===")
+import os
+original_cwd = os.getcwd()
+os.chdir(temp_dir)
+
+result2 = runner.invoke(cli, ['cache-clean'])
+print(f"Exit code: {result2.exit_code}")
+print(f"Output: {repr(result2.output)}")
+
+# Check what remains
+cache_files_after = list(cache_dir.glob("*.ast.json"))
+print(f"Cache files after: {len(cache_files_after)}")
+
+os.chdir(original_cwd)