As far as my googleing has led me I cannot find the source for GitHub anywhere, so unless (and I might be wrong) I missed something I think the platform is closed sourced.
That would not concern me much, but given the recent hype in the media regarding influencing developers to release their software as open source, and the number of open source projects they host etc I find a bit bothersome.
On the one had there can be no doubt that they are providing a great service for open source projects, on the other hand as a figurehead of opensource they might not be the best choice.
Although the code and code history is open, in that you can download it easily. Other data used by GitHub is less so. For example to backup the Issues you have to use the API to pull them each down. There's no easy way to download the fork network for a project.
If GitHub plans to remain closed source I'd like to see them provide a better backup option like Google Takeout or Facebook's data download.