I\'m not looking for this answer, because my question is different.
When I type vagrant global-status I get a list of vms, but some of those directories and
vagrant global-status
--prune didn't work for me. I removed ~/.vagrant, ~/.vagrant.d and .vagrant. And manually removed lingering VMs.
--prune
~/.vagrant
~/.vagrant.d
.vagrant
I migrated back gems and boxes from original ~/.vagrant.d. Perhaps one can try only removing machine from .vagrant but I didn't test that.
gems
boxes