While Horvath characterized much of her woes as being gender-related [1], the investigation could have classified most of them as either unprovable or terrible-but-not-provably-sexist (in particular, the behavior of the Preston-Werners).
I doubt it will ever be clear what actually happened. Theresa Preston-Werner's response [2] spends more time avoiding topics than actually covering them. Tom Preston-Werner likewise [3] makes sure to reinforce the fact that GitHub is immune to lawsuit while providing no real details. I'm sure there are plenty of GitHub employees who have a strong opinion, but enough of them seem to have an ax to grind in one way or another that it's hard to trust that testimony.
[1] http://techcrunch.com/2014/03/15/julie-ann-horvath-describes...
[2] https://medium.com/p/2fe173c44215
[3] http://tom.preston-werner.com/2014/04/21/farewell-github-hel...