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.]

Wow. I didn't know the gamergate thing went down like that. Apparently your repos on github can just be deleted at the whims of the employees...

Overall github is great but they definitely have some Growing up to do as an organization.

Either these takedowns need to be documented in the report, or the reasoning should be on the repo itself (i.e. "broke rule x" or "offended too many users" (which hopefully isn't a reason something is taken down)).

GitHub seems to be following the Reddit moderation style of "nothing that's illegal, or against our rules, or stuff that makes us look bad which we decide when we get grumpy emails"