I am using the 'Automatic Generator' of GitHub Pages, and I see it only generates a single index.html and other web resources.
How it works if I want to have a multi-page website generated from other markdown files?
You can get github to generate .html files from .markdown files by ensuring the top of the .markdown starts with the ---- block like this:
---
title: This will be used as the title-tag of the page head
---
hello
=====
**You are here!**
Found this here: http://xlson.com/2010/11/09/getting-started-with-github-pages.html