system-helper: Correctly copy the system config when modifying a repo
system-helper: Correctly copy the system config when modifying a repo

We were accidentally using the passed in copy of the rest of the config
when we should be using the one we read.

handsome-feng/flatpak,flatpak/flatpak,flatpak/flatpak,handsome-feng/flatpak,GeorgesStavracas/flatpak,GeorgesStavracas/flatpak,matthiasclasen/flatpak,GeorgesStavracas/flatpak,amigadave/flatpak,amigadave/flatpak,amigadave/flatpak,matthiasclasen/flatpak,handsome-feng/flatpak,handsome-feng/flatpak,flatpak/flatpak,flatpak/flatpak,matthiasclasen/flatpak,handsome-feng/flatpak,GeorgesStavracas/flatpak,flatpak/flatpak,matthiasclasen/flatpak,GeorgesStavracas/flatpak,amigadave/flatpak,matthiasclasen/flatpak