Fully calibrate Cobras

As reported in INSTRM-2699, convergence is getting bad. We updated the geometry made a new motor map (INSTRM-2609), but we still see a part of Cobras don't behave well (INSTRM-2718, INSTRM-2719). It's been almost 5 years since the last calibration, cloomis , chyan suggested to fully calibrate cobras. Calibration will be done for

1. Frequency
2. On-time
3. Motor-map + geometry

In this order. We should remember and save concrete procedure and scripts/notebooks for future.