To describe myself as upset right now is a major understatement. One of the major justifications to adding Whonx to Qubes was that much of the updating and maintaining of VMs would be handled by the Whonix templates within Qubes. Now, we find that this totally untrue.
I spent two hours downloading and installing regular updates and dist upgrades and only at the very end when I get this error message do find out that I did it all wrong. Worse, now that I am root there are packages to be installed that I just auto-removed when I was updating as non-root because that it what the upgrade program told me to do. I want to cry.
Not everyone is a forum junkie. Not everyone keeps up to date on what Whonix is doing. We should be able to rely on the regular update process to upgrade Whonix without any special instructions to following Qubes has an updater, use it!
If the net result of using Qubes with Whonix is that one has to go through the exact same nonesense to upgrade that one has to under KVM or Windows I'd rather go back there--all I have to do then is download the new release and start all over again. The amazing thing is that is would have been faster to download gigbytes over clearnet than all this non-sense over Tor and I doubt sincerely that I would be less safe.