commit: safer commit creation with reference update

The current version of the commit creation and amend function are unsafe
to use when passing the update_ref parameter, as they do not check that
the reference at the moment of update points to what the user expects.

Make sure that we're moving history forward when we ask the library to
update the reference for us by checking that the first parent of the new
commit is the current value of the reference. We also make sure that the
ref we're updating hasn't moved between the read and the write.

Similarly, when amending a commit, make sure that the current tip of the
branch is the commit we're amending.