Many documentation improvements

[jamesbraza]

• Open Source LLM Server #378 reveals that our docs here were incorrect
• Our docs were getting big so I added a Table of Contents
• Closes CLI functionality in Python module #402
• Adds LitQA v2 docs for Eval paper-qa 2 on lit qa 2 #413
• More logically groups sections

There is still a ton of room for growth here, but this is a good start

[whitead]

Thank you so much!!! Approving so we can just get this done and we can iterate more in future PRs