Fix Puppet 3.6 or later, manifestdir is deprecated, use manifest

Puppet (warning): Setting manifestdir is deprecated. See http://links.puppetlabs.com/env-settings-deprecations
   (at /opt/boxen/repo/.bundle/ruby/2.0.0/gems/puppet-3.6.1/lib/puppet/settings.rb:260:in `block (2 levels) in parse_global_options')