Always check filename in CI

Also ran the script to fix existing file names.

I found two errors which I handled manually:

• org.maui.shelf.md used org.kde.nota as app id (upstream PR)
• noappid.savoirfairelinux.jami-client-gnome.md (Gnome) and net.jami.jami.md (Qt) use the same app id

Further, I noticed that we are using the metadata from the Librem 5 fork for GNOME 3.24 of GNOME Settings instead of the original and up to date one.