packup does not respect package-archive-priorities

[cg505]

This needs more investigation, but it seems like our current approach in packup for checking/installing updates disregards package-archive-priorities (set in lisp/package/repositories.el). Namely, I see many packages on my system are installed from MELPA despite also being available in MELPA Stable (which has a higher priority).

This may be best wrapped into #84 (which would be lovely to finally get finished up when someone has a change).

[cg505]

Sort of unrelated but also might need more investigation: handling updates of dependencies (even if the package which depends on it has not had an update).