Made documentation link more prominent and adjusted language for brevity and clarity
Made Docs link smaller

The Documentation link was a bit too in your face. There doesn't seem to be a happy medium between ~~~~ (sub-heading) and **text** (bold), so I went with bold which is more subdued.
Added in-line links to docs for each feature referenced in Readme
Added short paragraph on contributing to drive people to the Development page.
Left out a word :x
Added section on contributing to docs including how to build local docs
Reference does not work without a colon
Added variable names to new 'writing documentation' sections
Updated 'feature list' links to use references rather than static deep links
Added reference variables to Models doc
Updated 'read the damn docs' link styling so the URL is clickable
Removed link to 'usage/transforms' doc which was missing
Added additional variables for TOC page
Adjusted reference variable to match standards set in docs/api/*
Added link at the end of each Usage doc to get to the API definition in case you want to find out more
Forgot blank line at end of file
API pages now link back to Usage pages for people who want to see examples of usage
Fixed warning about transforms.py by inserting newline at end of file
Fixed small typo
Removed 'Usage' and 'Learn More' from index toc's