FlatpakInstallation: Mark non-transaction install/update ops deprecated
FlatpakInstallation: Mark non-transaction install/update ops deprecated

These versions still work, but they don't do neearly as much as you'd
want (depdendencies and whatnot), so document this.

flatpak/flatpak,flatpak/flatpak,flatpak/flatpak,flatpak/flatpak,flatpak/flatpak