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.
Actually, anything that uses the Vagrantfile should automatically migrate your settings and custom boxes file. That means vagrant up and others should also do the right thing.
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