ORAC
"a super-secret installation just outside Alice Springs -- remains cloaked in secrecy."
Pine Gap is NOT super secret anymore. A fair bit of what goes on was disclosed in a book written by a person who works inside and all of it was fully approved before release with more detail than people thought. The media however like to blow it up as "super secret".
As to whether JOHR was working, we don't need to be told, as long as the relevant information is passed on which it would have been.