To emulate git, stash should not remove untracked git repositories
inside the parent repo, and checkout's REMOVE_UNTRACKED should
also skip over these items.
`git stash` actually prints a warning message for these items.
That should be possible with a checkout notify callback if you
wanted to, although it would require a bit of extra logic as things
are at the moment.
Any well-behaved program should write a descriptive message to the
reflog whenever it updates a reference. Let's make this more prominent
by removing the version without the reflog parameters.
