deploy: Clean up leftover state before creating new directories

This fixes a regression introduced with https://git.gnome.org/browse/ostree/commit/?id=7baa600e237b326899de2899a9bc54a6b863943c

The original code in "ostree admin upgrade" had a comment:

 /* Here we perform cleanup of any leftover data from previous
  * partial failures. This avoids having to call gs_shutil_rm_rf()
  * at random points throughout the process. */

But since I deleted that initial cleanup call, we *do* need to do the
cleanup during the process run.  It turns out there are only a few
places this is necessary.

https://bugzilla.gnome.org/show_bug.cgi?id=733030