Since the first public release, moteus has always calibrated motors so that a positive command is equivalent to a fixed sequencing of the phase wires. That means that depending upon which order you solder the phase wires, a positive commanded velocity will result in the motor spinning either clockwise or counterclockwise.
As it turns out, since moteus has an absolute encoder that is immune to such vagarities, it is much more convenient to normalize the direction of rotation around the encoder rather than the phase wires. As of release 2021-04-26, and moteus_tool 0.3.22, that is exactly what moteus does.
Now by default, moteus_tool will attempt to calibrate the motor such that a positive command results in a positive encoder value (this will be clockwise rotation when looking at the front of the motor / back of the moteus board). If the firmware is too old, it may not be able to do this, in which case it will emit an error.
You can also, use the new ‘--cal-invert'
option, which will have moteus calibrate the motor such that a positive command results in the encoder moving in the negative direction. For some existing deployed systems, you must use this option if you want the calibrated motor to have the same sense of direction as before (even with old firmware). As before, if this is not possible because the firmware is too old to support the necessary configuration, an error is emitted.