Repo reorganization to adhere conventions.

As a pilot to the repository conventions, here are the changes which would make this repository adhere to the conventions.

Please review with care and let me know your thoughts and comments. If you feel lucky with it, pull into master.

Noteworthy: I personally think that a master task file (such as `makefile`) should be always on top-level. I tried to resemble this with the `makeme.sh` file (sort of).