After the system upgrade, I found out that the websites hosted on my machine were down.
So, first of all, my apache2.conf file was restored to default (and I had to modify it again). Secondly, site-available files now must have the extension '.conf', so I had to rename all of them and use a2ensite to enable them again.
Next, one site shows a console error
ReferenceError: $ is not defined
I know it seems that the site isn't loading jQuery properly, but it worked before and stopped after upgrading, so I guess something else has changed. The upgrade affects jquery too in some way I cannot see?
UPDATE: seems something related to php. Jquery was called in a separate page, called through a require('pagename') and the required seems not to be interpreted.