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Cropping the final integration should be part of the normal flow
What I mean is that the cropped file should automatically be the next one you are working on, just like with background calibration, start colours etc. You crop because some part of the image is bad and you don't want that be part of the integration at all.
If you could explain this one a bit more that would be great, maybe with some screenshots? As in, why wouldn't you just crop at the end anyway?