Documentation is in a flat file structure

The documentation in the Wiki was had all the files in one directory. This should be cleaned up and organized into a tree of directories that are organized in some logical way.

## Definition of Done:
- [ ] Create a Style Guide
- [ ] Add a file naming convention to the Style Guide and strictly follow it
- [x] Organize all files reachable from the nav or index.md into a tree file structure
- [ ] Figure out what to do with files not reachable from the nav or index.md (include or delete)
- [x] Ensure that all links between files are updated and working correctly, including breadcrumbs

Start by reviewing the Wiki files reachable from nav or index.md and the current navigation structure. Define the file tree and naming convention in a Style Guide, then decide whether unreachable files should be included or deleted. Done means the documentation is organized, all links and breadcrumbs work, and the remaining checklist items are complete.

Written by the indexing model from the issue text.