In summary, my changes do away with the root puphpet.yaml in favor of the intended config location, there is no longer a needed to move files around (deizel@642ea88), and by deleting the default config.yaml there isn't a chance of it getting wiped out during updates.
Needs some more testing/documentation before merging.
In relation to #14, here are the changes related to the folder structure (and some PSR-2 formatting):
Needs some more testing/documentation before merging.