Refactor: CLI and Proxy

[dmarvp]

Summary

We want to restructure the way in which our docs are, starting with the CLI and Proxy. A new structure was defined here:

https://drive.google.com/file/d/16ihLEvOQp3eynL-hhCJjJqQ_TyI47RSx/view?usp=sharing

Along with the document, you'll find a lot of comments on which current sections need to go, altered or added.

[dmarvp]

The latest PR is still missing the FAQ section.
Also, we need to include something about the HTML reports in the CLI section.