feat(flattener): implement file discovery and filtering logic

Add file discovery and filtering functionality to the codebase flattener tool
- Use glob and minimatch for pattern matching
- Support .gitignore patterns
- Generate basic XML output with file count

.gitignore

@@ -28,4 +28,10 @@ sample-project/*
 .bmad-creator-tools
 .gemini
 .bmad*/.cursor/
-web-bundles/
+web-bundles/
+docs/architecture/
+docs/prd/
+docs/stories/
+docs/project-architecture.md
+tests/
+custom-output.xml