Squash a few smalls bugs, other tweaks.

Added a loop for the basic setup of vms so the user can make sure things are
going ok, and fix them if anything is amiss. We might want to conditionalize
this if/when we are confident enough in no errors on an unattended run.
Merge pull request #2 from jguiditta/fix_havms_setup

Squash a few smalls bugs, other tweaks.