The closest thing I've found is this SOF topic:
http://stackoverflow.com/questions/4779582/markdown-and-including-multiple-files

Which references this sample project at hithub:
https://github.com/akmassey/markdown-multiple-files-example

Summarizing: you can split the documentation into several pieces, but you'll need to execute a script in order to get a joined doc file in the local repository. Winthin github, the documentation will appear splited into those pieces.