fixed broken bits, removed cruft and redundancy

The cleanup.sh script did a bunch of unnecessary removals which resulted
in grub and NetworkManager being removed. Doing the latter broke
networking. This has been removed from cleanup.sh.

The vagrant user setup happened twice: once in ks.cfg, once in vagrant.sh.
Since it's necessary to do the setup in ks.cfg since otherwise the other
scripts can't run, I kept that one and removed vagrant.sh.

The gem-based install of chef was broken due to a missing dependency. I
switched to the Omnibus installer so we don't have to worry about those.