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I do not see why this should not work from MoveIt's point of view. The stop-request is forwarded to the FollowJointTrajectory action-server that executes the trajectory. Whether this action server then aborts the trajectory is up to him. I seem to recall that ros-control based systems will still try to execute the rest of the trajectory even if they are asked to abort. So what implements your FollowJointTrajectory action server?

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