I would recommend that Ubuntu either uses the Debian package as-is, or
branches from the Debian packaging to apply whatever divergence is
desired. I'd be happy to let Ubuntu maintainers of flatpak use the
`ubuntu/*` namespace on Salsa for this, similar to how gnome-shell is
packaged.

Obviously I'm only a Debian and upstream maintainer of Flatpak, and not
an Ubuntu developer; if Ubuntu people want to diverge, that's their
choice to make, although I would encourage prospective Ubuntu
maintainers to consider the maintenance cost of divergence before
diverging.

> - unix 'wheel' group users can install and remove packages from configured
>  flatpak remotes, without password

Where are you getting this from? From upstream, or from Ubuntu
packaging?

The upstream default is the wheel group, but the Debian packaging
configures flatpak `--with-privileged-group=sudo`, which should mean
that the privileged (root-equivalent) group is `sudo` rather than
`wheel`. I would hope that Ubuntu inherits that configuration change.

> As such, installation of new apps via flatpak should use polkit to authorise 
> the transaction -
> whilst upgrades should not.

Deleting the custom polkit policy
(/var/lib/polkit-1/localauthority/10-vendor.d/org.freedesktop.Flatpak.pkla
and/or /usr/share/polkit-1/rules.d/org.freedesktop.Flatpak.rules,
depending which polkit version Ubuntu is using) might be enough to get
this behaviour. Please see
/usr/share/polkit-1/actions/org.freedesktop.Flatpak.policy for details
of what will happen if those files are deleted.

Please bear in mind that upgrading an app might require installing a new
runtime for it to run on (for example, upgrading org.gnome.Recipes might
switch its required runtime from org.gnome.Platform//40  to
org.gnome.Platform//41, or upgrading com.valvesoftware.SteamLink might
switch its required runtime from org.freedesktop.Platform//20.08 to
org.freedesktop.Platform//21.08), so even if
org.freedesktop.Flatpak.app-install requires authentication, it might be
desirable for org.freedesktop.Flatpak.runtime-install to not require
authentication.

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https://bugs.launchpad.net/bugs/1943480

Title:
  flatpak installation permission requirements different from ubuntu
  software

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