When starting a new repository, it does not have any branches
in `.git/refs/heads` and `.git/refs/HEAD` contains a broken
`ref: refs/heads/master` reference.
This means that cloning a repo like we do for cleaning will fail
with very unhelpful message for freshly created repo:
fatal: bad revision 'HEAD'
This is quite confusing when you create a new repo by copying
Nix files from another, working one, make some trivial changes,
stage them and then try to test a shell.
