For details of an LibrePilot development environment please refer to the Development Manual https://librepilot.atlassian.net/wiki/display/LPDOC/Linux+-+Building+and+Packaging.
If you would like for VirtualBox window to open, this can be useful for running apps, set 'vb.gui = true' in Vagrant file. For now the vagrant shell (ssh) will not work when starting in GUI mode.
Once your machine has started up you can ssh into it or log into Xfce (assuming you set vb.gui = true). Any changes you make persist in the Vagrant VM, when you are done run 'vagrant halt', this will turn off the vm and persist your changes.