Removing top-level folders to force all content into environments

Should make for easier version control if all modules, manifests, etc.
are in a particular environment, and each environment is tied to a
particular VC branch.
Attempt to minimize puppet.conf
Final cleanup on puppet-generic.conf
Forgot to change site manifest path
Forgot other entries for site.pp
Why not run 5 times to configure puppetdb, just to be safe?
Final cleanup before merge