questions about trajectory_msgs/JointTrajectory.msg

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There are three joints here, my question is which joint has the trajectory such as points [..]

With three joints, the message you show encodes a single trajectory with a single point (the points list contains only a single entry).

That single point has three values in each of the positions and velocities fields, one for each joint.

There is a problem though: names contains three (3) elements, while both positions and velocities contain four (4). That is invalid (the fourth value will be ignored by consumers).

How to specify all three different joints' trajectory using the command above?

If I understand you correctly: just add more entries to the points field (which is a list). Something like the following should work:

{
  "joint_names": [
    "RKneePitch",
    "RHipPitch",
    "RHipRoll"
  ],
  "points": [
    {
      "positions": [ .. ],
      "velocities": [ .. ],
      "time_from_start": [ .. ]
    },
    {
      "positions": [ .. ],
      "velocities": [ .. ],
      "time_from_start": [ .. ]
    },
    {
      "positions": [ .. ],
      "velocities": [ .. ],
      "time_from_start": [ .. ]
    }
    ,
    ...
  ]
}

be sure to update time_from_start for each point.

See also the documentation for trajectory_msgs/JointTrajectory and trajectory_msgs/JointTrajectoryPoint.