deploy: Copy parent directories for modified config files

deploy: Copy parent directories for modified config files

Previously, in the case where a parent directory of a modified config
file was removed, we would throw an exception.  This happens when
switching from a tree that has some software (e.g. firewalld), to one
that does not.

While it's nice to have this warning that your config file probably no
longer applies, there's no need to make it so...fatal.

It's particularly problematic that the only easy workaround is to
remove the config files from your current tree - which breaks
rollback.

The solution then is for for us to take ownership of the parent
directories too into the new /etc.  Admins can clean up these files
afterwards at any time.

https://bugzilla.gnome.org/show_bug.cgi?id=734293