add TOC and slight reorganisation

[bbartholdy]

Hi Ben,

This document is getting quite large (which of course is awesome!), so I thought it might benefit from a table of contents.

I updated all headers from **Header** to ## Header to be compatible with a TOC auto-generator, and rearranged the Reproducible research section to have 'Writing reproducible manuscripts' as a sub-section.

[benmarwick]

Thank you so much, this is great! Please also add yourself as a contributor!