If you try to: organize: /usr/bin/python3.5: "/usr/bin/python" You'll get: Trying to organize file '/usr/bin/python3.5' to '../../../../../../../../../usr/bin/python', but '../../../../../../../../../usr/bin/python' already exists If instead you try: organize: /usr/bin/python3.5: "python" You'll get: [Errno 13] Permission denied: '/usr/bin/python3.5' The correct approach is to use relative paths: organize: usr/bin/python3.5: "usr/bin/python" I can't imagine why you'd want to organise absolute paths. Maybe we should disallow it altogether? Failing that, can we warn?