Since everyone is always going to do this process every time they wire things up, the software should have a wizard to walk you through the process! With motor disconnected, connect encoder wires, manually rotate (right hand screw rule); software can detect saw tooth; tell used to swap wires if required; connect motor wires; ask for max current etc etc
Thank you for the suggestion, we totally understand the pain here. You can use the "calibration wizard" in Motion Terminal. It's in the section 1.3.2. It's a Software Solution, and we are working on a more robust and complete way directly execute in the firmware, in the core of the Units, fully simplifying this activity.