From what I can see, it looks like GitHub employee @jakeboxer explicitly took the GamerGate one down to satisfy a feminist called @nexxylove because she claimed it contained "stalking and harassment" documents. http://imgur.com/AgSwrE2. This is the same individual claiming to be "astounded and really fucking angry" at the Intel/Gamasutra fiasco part of Gamergate (http://i.imgur.com/l1Uwkvd.png)

Yep, not evident from the transparency report that repos get taken down so casually, with other users protesting. [I'm guessing it probably didn't contain those sort of instructions, and they can't claim so in the transparency report, because that would be libelous.]