core: check that extensions have the hierarchies before overlaying

core: check that extensions have the hierarchies before overlaying

Before confext was added, hierarchies always existed in extensions. Now
they are optional - i.e., a sysext will not contain /etc/. So mixing a
confext and a sysext fails, as we'll try to create an overlay with /etc/
from the base, the confext and the sysext, but the latter doesn't have
the directory.

After the source images are mounted, check that each hierarchy exists in
each source image before creating the overlay, and drop them if they
don't.

Follow-up for 55ea4ef096543