Our logic to decide if a file needs to be checked out from the previous commit
or deleted because it didn't exist in the previous commit didn't work for
submodules. We were using `git cat-file -e` to ask whether the file existed, but
this returns an error for submodules, so we were always deleting those instead
of reverting them back to their previous state.
Switch to using `git ls-tree -- file` instead, which works for both files and
submodules.
c1e52fc807