use skip-arches to clean refs off repo

[ramcq]

If skip-arches is added to a .json when it has previously built on that architecture, that means the old ref for a previous build on that architecture (even if it's not useful) remains in the repo, and won't get updated again. When updating the repo we should use the skip-arches list from the flatpak to clear the refs, or if it's easier, just clear the refs for all of the arches that we're not publishing.