`JujutsuPatcher.apply_patch_for_empty_files()` was matching all files with "new file mode" in the diff, not just truly empty ones. After the `patch` command correctly created new files with content, `apply_patch_for_empty_files()` would then overwrite them via `make_empty_files()`, truncating them to zero bytes. The fix skips files that already exist on disk (created by `patch`) so that only genuinely empty files (which `patch` can't handle) get created. Testing Done: - Applied a patch that added new (non empty) files. - Ran unit tests.