Marek, I possibly found a way to reproduce some of the issues here regarding the Qubes tools issues in the templates/AppVM's that is causing haywire on some Qubes 4 systems out there (and a way to solve it too). It's a user mistake, and quite frankly, quite an embarrassing one at that. Nonetheless, perhaps it might be a good idea to help make it harder for other users to repeat the same mistake, if feasible or desired of course.
It's triggered by restoring Qubes 3.2. templates in Qubes 4 (face-palm moment, I know), which without knowing the code I'm guessing is different between the Qubes 3.2. and Qubes 4 releases. I did not think much of it at the time, and it was easier to just restore everything, like go take a break or sleep while it works, instead of typing -x AppVM -x Template, etc. exceptions into the command line. I mean, if the computing time is irrelevant and you got plenty of disk space, it may be tempting to just restore it all while you go and do something else. Perhaps it'd be good to have something that stops the restoration of Qubes 3.2. templates, or a message that warns people in place before it goes out to people that might make same user mistake.
Somewhere down the line, one of the old Fedora templates from my 3.2. system was not deleted after restoration, and same user mistake happened on more than one machine.
After I re-linked all my AppVM's over to Qubes 4 fedora templates, it has for now worked pretty smoothly for several hours now.
I'm not sure if having to delete the old template was part of the solution, or if it made any difference, but I deleted it right away before testing that, perhaps I should have, but you probably know if it matters or not.
Creating shortcut issues in the Xfce4 menu is still for some AppVM's broken, but I'm suspecting creating a new AppVM and manually transfer userdata over might be able to fix that (Will try when I have the time). Seemingly old backup AppVM's are the ones with broken shortcuts? I haven't had time to test this, but it appears like that.
Also,
Chris Laprise over at
https://groups.google.com/forum/#!topic/qubes-users/Dxe8-0vaIuk found an easy way to solve the re-install of debian-8 issue. But this did not solve the qvm-run or qvm-open-in-vm issues for debian, at least not for my system, and possibly maybe others out there.
In short.
- Deleting 3.2. fedora templates and re-linking to Qubes 4 fedora templates only, appears to fix the qvm-run / qvm-open-in-vm issues in fedora templates.
- Re-installing Debian works with provided solution in the link from
Chris Laprise posts over at the link above, but qvm-run or qvm-open-in-vm are still broken in debian.
- Some systems have a working debian template, while other systems do not. Is this hardware specific issue perhaps? Random? or different setting during Qubes 4 install maybe?