support windowed option in detrend.py and runIsr.py

PIPE2D-914 adds a config option -c windowed=True to support windowed reads. Please make this work for the other command line options too. It also needs to work if we're running just IsrTask (although admittedly we could just set overscanFitType = "MEDIAN", but that seems like something that we don't want users to know.

I'll push my version that does this, but price may not like the way I did it as it copies some of the windowed magic into multiple places.