While trying to reinstall some templates my dom0's application menu just broke, 
with every .desktop file gone.
I wanted to document how to fix this for others - use this command:

sudo qubes-dom0-update --action=reinstall $(rpm -qa | grep 'qubes\|xfce4' | 
grep -v 'template\|kernel')

What it does is the following:
Get a list of installed packages,
filter for those of Qubes or xfce,
filter out any templates or the kernel,
and then reinstall them.

This should restore all the desktop files and with that your application menu.

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