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base_link (or base_footprint depending on your configuration) should go at the rotational center of the robot, i.e. the point about which the diff drive robot can spin-in-place. This assumes that base_link is the frame you will be using to command velocities relative to.

I don't know if this is actually explicitly stated anywhere, but it's how I've always configured move_base.

Note that you can always make another frame called "geometric_center" or something similar and publish a transform between that and base_link if you would prefer other transforms relative to the geometric center of the robot instead of the center of rotation.