Update auto-complete from MELPA
Update flycheck from MELPA
Update helm from MELPA
Update magit from MELPA
Update php-auto-yasnippets from MELPA
Update puppet-mode from MELPA
Update skewer-mode from MELPA
Update smartparens from MELPA
Update web-mode from MELPA
Pull a few related things into nateeag-load-path.el

It needs to be renamed now.
Refactor nateeag*.el files into site-lisp/bootstrap.el

I feel slightly better about the universe now.