Move the Makefile to the root of the repo

I might just be being picky, but I prefer the Makefile being in the root of the repo, not in src. Feel free to reject this if it breaks a convention or something.

__Note:__ The Makefile's location is updated in everything but the Dockerfile (I don't know Docker, so I figured it would be safer for me to leave the fix to someone else). If you plan on merging this, please fix the Dockerfile.