Deleting an OWNERS.yaml file without staging the deletion leaves it in Git's index, causing CODEOWNERS generation to try to open a missing file. Exclude deleted paths from the file scan while preserving tracked and untracked files, including dangling symlinks.

Regression tests cover staged and unstaged deletions and verify that files still present remain included. All seven tests in the changed-files module and the CODEOWNERS generator smoke test passed; both Python files pass Ruff formatting checks. `bazel run format` could not complete because its Rust helper failed to link on macOS (`library 'System' not found`).