(SERVER-138) Created puppet.conf differences doc

This commit introduces a new document which contains some information
about the differences in supported settings from the `puppet.conf` file
for Puppet Server as opposed to the Ruby-based Puppet master.
I like that these are in a separate section from the other settings. If we do end up documenting these I think they should stay in their own section, with a note saying that while these settings are not honored by Puppet Server they will still be honored by Puppet Agents.