High: VirtualDomain: save the config before virsh undefine (bnc#891915)

virsh undefine removes configuration files if they are in
directories which are managed by libvirt. VirtualDomain didn't
include the undefine call before, so this wasn't an issue until
recently.

Directories considered managed by libvirt also include
subdirectories of /etc (for instance /etc/libvirt/*).