The files created by GenerateScale should be lowercase, and should maybe go in a separate subdirectory to avoid clogging everything up.
We should reevaluate which of the files are actually useful to save (e.g. I suspect that the masked ones don't need to be), and which aren't. Alternatively, could have a keyword to save all files.
Radii at which scaling was done should be written into filenames
should be named in the form scale_factors_XXtoYYpix.fits not RATIO_LIST.fits. Really should just specify output name for scale factor file.