Reintroduce the apt_update_run flag, which prevents apt-get update after `vagrant halt`

Provisioning runs again on `vagrant up` after `vagrant halt`, on `vagrant reload`, and on `vagrant provision`. In these cases, we should not need to run `apt-get update` again, as all packages installed by apt will persist through shutdown and boot.

This creates a file in the guest OS's tmp directory that persists until the vagrant box is destroyed, at which time the full provisioning script will run again.

Closes #37