(Ironically fgrun , which does use both branches, doesn't have such a notice. I have not checked the other add-ons.)
Like James said, we switched the FGRun repo to next two weeks ago. It now correspond to the FlightGear and SimGear repos. Since the switch was very recently, the master branch looks "active", but it's not ;-) At the same time, I've also changed the versioning scheme to follow FlightGear/SimGear's version numbering.