I've been using App::GitGot to manage my development directory across machines and moving to a new(ish) box I ran "got update" to pull down all the repos and got the above error.

I fixed it by changing _get_clone_or_callback in App::GitGot::Commands to not create the directory before trying to clone and passing $entry->path as the second parameter to $entry->clone() … but I'm not sure that's the best solution overall.