Move flymake-init.el out of project root
Move php-mode-init.el out of project root
Move flymake-php-setup.el out of project root
Move autopair-init.el out of project root
Move auto-complete-init.el out of project root
Move yasnippet-init.el out of project root
Remove byte-cache directory, as it is unused
Add site-lisp/ to load-path

I didn't realize it wasn't there, and come to think of it, this may
explain the strange bugs I was having with autoloading my python-mode
accessories...