manifest dir/

Reverting back to having a manifest/ dir for site.pp. This is possibly the
'least suprising' config.
modules/ dir

Planning to use this as a location to store modules currently being tested
before migrating them to Puppetfile. The path is added to Puppet as a
basemodulepath component before running puppet apply
Vagrantfile updates

* r10k will now only install modules from Puppetfile if /etc/puppet/modules
  does not exist
* Simplified paths by removing Puppet environments, now using basemodulepath
Vagrantfile fixes

* Better, actually working check if /etc/puppet/modules is empty
* Default to run puppet apply without --debug
Work in progress GA