vmimage.subr: Add missing directories to METALOG

Theoretically METALOG should include everything which needs to go
into disk images; unfortunately there are still a few bugs which
are resulting in directories not being listed -- and if METALOG
has files in unrecorded directories, the directories end up being
created with 000 permissions.

Oddly enough, systems where / has 000 permissions are not very
usable.

As a temporary hack, compare the staging tree against METALOG and
add entries for any unrecorded directories. This will hopefully
be reverted before 15.0-RELEASE.

Reviewed by: bapt, emaste, ivy
Sponsored by: https://www.patreon.com/cperciva
MFC after: 5 minutes
Differential Revision: https://reviews.freebsd.org/D53153