lib/checkout: Add bareuseronly_dirs option

lib/checkout: Add bareuseronly_dirs option

This is a continuation of https://github.com/ostreedev/ostree/pull/926
for directories instead of files.

See: https://github.com/flatpak/flatpak/issues/845

This option suppresses mode bits outside of `0775` for directory
checkouts.  I think most people should start doing this by default,
and use explicit overrides for e.g. `/tmp` if doing a recommit based
on a checkout.

Closes: #927
Approved by: alexlarsson