run: Fix completion for --system/--user
run: Fix completion for --system/--user

These options were not showing up in completion,
and, if present in the commandline, would prevent
further completion, despite being accepted by
the run command.

Closes: #2534
Approved by: alexlarsson

flatpak/flatpak,flatpak/flatpak,matthiasclasen/flatpak,flatpak/flatpak,matthiasclasen/flatpak,flatpak/flatpak,matthiasclasen/flatpak,matthiasclasen/flatpak,matthiasclasen/flatpak,flatpak/flatpak