Cleanup Root Directory

**Describe the solution you'd like**
There's a lot of unnecessary files that are muddying our root directory structure and should be cleaned-up in order to make it easier for other people to read the directory structure.

A couple action items:
- [ ] Determine what can be removed from the root directory and what needs to be re-organized
- [ ] Cleanup the directories

Start by inventorying the repository root and identifying which files and directories are unnecessary or belong elsewhere. Determine the intended root layout before changing anything. Done means the root directory is cleaned up and reorganized without removing items that are still needed.

Written by the indexing model from the issue text.