Today it’s my turn. I have done a very dumb thing and my system became basically broken.
TL;DR Removed core packages in Qubes. Had the system almost unusable but managed to fix the issue. I’m posting here just to share the experience in case anybody sees themselves in this situation in the future.
What made it break?
I was removing a dom0 package, which I thought was non-essential (xwininfo).
When removing the package it asked for confirmation:
[user@dom0 ~]$ sudo dnf remove xwininfo
Dependencies resolved.
========================================================================================================================
Package Arch Version Repository Size
========================================================================================================================
Removing:
ModemManager-glib x86_64 1.6.4-1.fc25 @anaconda 1.0 M
NetworkManager-wifi x86_64 1:1.4.6-1.fc25 @anaconda 137 k
Thunar x86_64 1.6.11-1.fc25 @anaconda 6.5 M
albatross-xfwm4-theme noarch 1.7.3-4.fc24 @anaconda 106 k
anaconda-gui x86_64 1000:25.20.9-17.fc25 @qubes-dom0-cached 1.7 M
anaconda-user-help noarch 22.4-4.fc24 @anaconda 152 k
anaconda-widgets x86_64 1000:25.20.9-17.fc25 @qubes-dom0-cached 93 k
bluebird-xfwm4-theme noarch 1.2-4.fc24 @anaconda 88 k
dzen2 x86_64 0.8.5-17.20100104svn.fc24 @qubes-dom0-cached 141 k
enchant x86_64 1:1.6.0-14.fc25 @anaconda 130 k
fros noarch 1.1-8.fc24 @anaconda 42 k
[...]
qubes-desktop-linux-common noarch 4.0.21-1.fc25 @qubes-dom0-cached 387 k
qubes-manager noarch 4.0.45-1.fc25 @qubes-dom0-cached 5.7 M
[...]
Transaction Summary
========================================================================================================================
Remove 107 Packages
Installed size: 199 M
Is this ok [y/N]: y
I must have been in autopilot. 107 packages removed and I typed yes 
Among other things there were packages like qubes-manager and qubes-desktop-linux-common.
What broke?
- couldn’t install packages - essential to revert the issue (see bellow)
- couldn’t backup - qubes-backup was uninstalled
- couldn’t start new qubes
qubes world start but their windows would not open. qvm-run also didn’t work. - window decorations broken
on qubes that were running (e.g. sys-firewall) but where I didn’t have any window open before, the colored borders started not showing up.
Couldn’t install packages
This was the key issue. For some reason it stopped recognizing packages:
note: the parts inside the
~~~~were in red and the rest was white (to symbolize they were running in sys-firewall)
[user@dom0 ~]$ sudo qubes-dom0-update wmctrl
Using sys-firewall as UpdateVM to download updates for Dom0; this may take some time...
~~~~~~~~~
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora-updates.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora-updates.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Invalid configuration value: failovermethod=priority in /var/lib/qubes/dom0-updates/etc/yum.repos.d/fedora-updates.repo; Configuration: OptionBinding with id "failovermethod" does not exist
Warning: Enforcing GPG signature check globally as per active RPM security policy (see 'gpgcheck' in dnf.conf(5) for how to squelch this message)
Last metadata expiration check: 3:26:04 ago on Sun May 23 05:07:54 2021.
Package wmctrl-1.07-19.fc24.x86_64 is already installed.
Dependencies resolved.
Nothing to do.
Complete!
~~~~~~~~~
Qubes OS Repository for Dom0 35 MB/s | 36 kB 00:00
No package wmctrl available.
Error: Unable to find a match.
note: just ignore the
failovermethod=priority. That has to do with another issue and should have no impact.
As you can see, first it says the packages is already installed but then No package available. As a result, you’re not able to install any packages.
Fedora dnf history undo also didn’t work because the packages were no longer cached and the dnf command doesn’t know how to get packages (only the wrapper qubes-dom0-update does).