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If your robot is position controlled, one strategy you can implement is to hold position when your RobotHW specialization initializes. With this I mean, before starting the control loop, read joint positions once and set those values as commands. This way, joints not associated to any controller will remain where they are.

Alternatively, and if your hardware allows for it, you can designate a special value (quiet NaNs are customary) to represent non-initialized values. With this approach, you don't need to read joint positions, but just initialize the commands to this special value before starting the control loop. In such cases, what to do when these values are received is HW-dependent, but for position-controlled robots, it typically means hold position.