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aha this is what makes it so much fun.
MA 4 lets you utilise the other branches to check stuff in... but when installing MA 4 onto 3.6 agents to have to have checked MA 4 into the current branch.
So you are still stuck with switching of the agent section of any deployment/update/global updating tasks before checking it in and then enabling this option bit by bit if you want to roll this out in a controlled manner.
but at least once you have MA 4 on the workstations you can use the other branches