Add configuration for Directory Environments

This work allows the the user to take advantage of directory environments by providing new params on the server config section and providing the logic necessary to remove old puppet.conf configuration items and replacing them with the new style configuration options.  Old config styles have been deprecated and will be removed in future versions of Puppet.
Oh cool, I'll happily make it default.  I actually wasn't sure the state of things and I'm way more happy being aggressive about deprecating old features when acceptable.