Update Reqstool docs

[lfvbarcus]

Summary

We should review and update the docs with some more examples on how reqstool runs.

Proposal

Update docs with some more explanation on how the data is used internally by Reqstool

[lfvbarcus]

@lfvmarcus Any insight from a fresh pair of eyes would be nice :)

[lfvmarcus]

I've read through the entire documentation now an the there are a few pieces of information I'm missing:

• How to annotate.
• What formatter and settings should used for JSON.
• The status results example output is missing the "Total" row.

Then there are formatting issues:

• None of the C4-diagrams seem to render.
• There are markdown links on the pages Start, How it works, Usage, Quickstart, and File and directory sets.