Another one suggestion: write user manual with the help of
Sphinx and maintain it in source tree. There is a free service
Read The Docs for hosting Sphinx-based documentation. It includes
deep integration with GitHub and automatic update of documentation on every commit (with the help of GitHub webhook). It also compiles documentation into PDF and EPUB formats.
There are downsides, of course. It will require Python for local testing of documentation, learning of Sphinx for documentation setup and learning of
reStructuredText for documentation writing (however, reStructuredText is close to Markdown).
I understand that user manual writing isn't a priority for now and GitHub wiki is pretty fine suited for current needs. Just wanted to describe one of other possible variants.