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Is there any indication that the owner took it down himself while claiming GitHub did it?

Where have the owner claimed that it was taken down?

As far as I know, the owner of JNDIExploit did not claim that GitHub took the repo down. I am trying to find their contact information to remove any doubts around this.

What if GitHub, is the owner?

yes https://news.ycombinator.com/item?id=29538540

Reply on news.ycombinator.com