As part of changes to Forklift, the Vagrant specific code has been moved to a vagrant/ directory with the exception of the Vagrantfile. Running vagrant status after pulling master should migrate custom box files and settings.yaml into the vagrant/ directory for you. If you experience any weirdness, please reply here so that we can fix any edge cases we missed.
You’re correct we didn’t think of an rmdir. I also had local boxes.d/tmp-80-*.yml files which it didn’t migrate but I think that for most uses the migration did what it had to do. For the rest this heads up did what it had to do