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The JointTrajectoryAction was used earlier for connecting to the arm controllers on the PR2. However, since it lived in a PR2 specific stack, we decided to move away from it so that other people using the motion planning pipeline would not have to depend on a PR2 specific stack. The FollowJointTrajectory action is intended to replace the JointTrajectoryAction. To preserve backwards compatibility both interfaces are currently implemented in the following controller: robot_mechanism_controllers/src/joint_trajectory_action_controller.cpp

Using this controller implementation on your own robot will take some work since it is tied into the way that the control infrastructure has been setup on the PR2. However, you can use the code in there and the actionlib tutorials as a guide to how you can implement a similar interface on your own robot. Essentially, you need to have an action interface on your robot that connects to your controller and respects the specifications laid down by the FollowJointTrajectory action spec (control_msgs/action/FollowJointTrajectory.action).

Hope this helps.