When you are patching complete directories, GenPatch will detect files that were renamed and modified automatically. This is accomplished by the Auto-detection of ideal creation paths which tells GenPatch the correct start states file for the renamed file.
This gives you the freedom to mostly not care about renamed files. Note though, that GenPatch does not include information to remove the old filename after creating the new version under the new filename. You need to enable the automatic cleanup for the patch file to remove the old version (actually move it to the backup folder) so that it no longer exists.