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I believe #9941 will answer your question, but please follow up if its not clear.

In short, the linear and angular components of twist messages represent the instantaneous linear and angular velocities. In most applications (that I have been exposed to), it is common to use the robot's body frame (e.g. base_link) as the default reference frame, because this is typically the frame you have control over. If you need that to be in a specific reference frame, you can use TwistStamped messages, which include the frame in the header.