lintian: modules-enabled files and a few others are non-compliant now

Lintian is now complaining. I forked the current master branch and pushed it unchanged to salsa. CI failed:

E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/apt/preferences.d/50freedombox3.pref
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/custom-shortcuts.json
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/apps
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/coquelicot
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/disks
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/expert_mode
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/lib
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/owncloud
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/packages
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/repro
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/restore
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/system
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/udiskie
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/modules-enabled/xmpp
E: freedombox: conffile-is-not-in-package remove-on-upgrade /etc/plinth/plinth.config
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/apt/preferences.d/50freedombox3.pref
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/custom-shortcuts.json
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/apps
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/coquelicot
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/disks
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/expert_mode
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/lib
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/owncloud
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/packages
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/repro
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/restore
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/system
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/udiskie
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/modules-enabled/xmpp
E: freedombox: non-etc-file-marked-as-conffile remove-on-upgrade /etc/plinth/plinth.config
E: freedombox: relative-conffile remove-on-upgrade /etc/apt/preferences.d/50freedombox3.pref
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/custom-shortcuts.json
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/apps
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/coquelicot
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/disks
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/expert_mode
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/lib
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/owncloud
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/packages
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/repro
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/restore
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/system
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/udiskie
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/modules-enabled/xmpp
E: freedombox: relative-conffile remove-on-upgrade /etc/plinth/plinth.config