I can't attest to ArXiv publication, I didn't consider it actually (I may now, though to be honest mine is not groundbreaking research by any stretch of imagination), but publishing the LaTeX source on GitHub is definitely relatively common. I and a few acquaintances I knew from my Master's program did that.
I imagine it depends on the field. Having perused your GitHub page and taken a look at what your program was about, I see why you might publish your thesis' source there. People working in theoretical physics aren't too inclined towards free software, so maybe that's why I haven't seen many related papers.
