I have a project together with several people and we have a README.md file with a bunch of GitHub Flavored Markdown that is rendered on our GitHub page. We also
I've recently made a package gh-pages-generator to solve this problem - it generates multi-page site using multiple MD files and a configuration file.
It correctly updates all the links between the pages. It's relatively easy to make it a part of CI to commit changes back to gh-pages branch.
I am using it here and here.