This SASS-ified Materialize Kit download is a php website that uses server-side includes for common components like header, navigation, and footer. You can reskin the app by merely changing the scss variables. The kit uses Grunt to compile and concatenate js and css files. Feel free to examine the grunt file and make changes as you see fit.
Materialize is heavy. I doubt you'll need customized plugins at all. Out-of-the-box components include: