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JointTrajectoryController is a good way to command trajectories even when you know only the desired joint angles. This will give you an insight on how the trajectories are formed and This will inform you about how they are interpolated. The key thing is to have a valid time_from_start in trajectory_msgs/JointTrajectoryPoint when you are filling the trajectory_msgs/JointTrajectory message.
Other way is to use MoveIT! which takes care of planning and collision checking and also takes care of IK, but personally I find it slow.