Documentation revamp

[bagashe]

Several small changes to make the documentation more readable to a technical audience.

1. Font is now slightly smaller with increased line spacing. Makes it easier parse large quantities of text.
2. Use horizontal screen real estate.
3. Color scheme that is easier on the eyes.
4. No navigation header. Uses a simple table-of-contents approach.

Added a link to the Nature paper and got rid of a couple pages that were no longer relevant.