Looks like if the master branch doesn't exist, git will not locally check out what we mark as the default branch (typically ubuntu/development-codename). This leads to what appears to be an empty folder and a frightening warning:
warning: remote HEAD refers to nonexistent ref, unable to checkout.
Apparently there's "a per-repo config flag we can flick on" says @tsimonq2. We (he) need(s) to do that.