Add source file hierarchy

First effort to move files into folders for the project. Before we can get to some new cool things for https://github.com/allending/Kiwi/issues/306, I would like to change some things around. It will also be easier for other people to contribute if the codebase is top notch.

The `Engine` folder is still pretty huge and generic with this PR, it will probably be split more logically later.