Is it possible to generate an automatic Table of Contents using Github Flavoured Markdown?
Github Flavored Markdown uses RedCarpet as their Markdown engine. From the RedCarpet repo:
:with_toc_data - add HTML anchors to each header in the output HTML, to allow linking to each section.
It seems in that you'd need to get at the renderer level to set this flag, which isn't possible on Github obviously. However, the latest update to Github Pages, it seems that automatic anchoring is turned on for headers, creating linkable headings. Not exactly what you want, but it might help you create a TOC for your doc a bit easier (albeit manually).