vagrant で "The working directory for Vagrant doesn't exist! This is the specified working directory:"

$ vagrant global-status
b7a606c  default virtualbox running /Users/koya/dev/Showtime/vagrant-nodejs-redis-mongodb
6d6c61f  default virtualbox running /Users/koya/vagrant/vagrant-nodejs-redis-mongodb
d99c027  default virtualbox running /Users/koya/vagrant/showtime/cookbook
4eec0aa  default virtualbox running /Users/koya/vagrant/showtime/showtime
4d2fcf8  default virtualbox running /Users/koya/vagrant/showtime/showtime-chef/cookbook

で使っていないマシンを削除しようと思って

$ vagrant destroy 4eec0aa 
The working directory for Vagrant doesn't exist! This is the
specified working directory:

/Users/koya/vagrant/showtime/cookbook

マシンを手動で削除してしまうとインデックスだけ残るらしい

$ vagrant global-status --prune

これで綺麗になる