The example Vagrantfile in this project can be kept in this folder, or moved anywhere else such as a project/site folder. Generally if you want to have multiple sites on 1 Vagrant VM, you should keep the Vagrantfile where it is (in the trellis dir). If you want to have 1 Vagrant VM PER project/site, you should make copies of the Vagrantfile and put them into each project's dir. You'd then run vagrant up from the project specific directory.