When using --no-checkout, the main repository would be confused about
the state of the submodules: Instead of considering them not checked-out
it would consider them checked out at their HEAD, yet with their index
cleared, so all files would look deleted and after `git wtas` you would
have to do:

git submodule update --init  # obviously
git submodule foreach git checkout HEAD -- .  # oh, ok

With this change, `git wtas` will take longer and may do superfluous
checkouts of files, but a `git submodule update --init` is all that is
necessary to get everything right.