Clean up (deprecated) cryodrgn preprocess codepaths/docs

[zhonge]

We recently removed cryodrgn preprocess starting in cryodrgn version 3.x, but we still need to clean up some of the deprecated functions and update the documentation.

Some of the cleanup was done in this branch that was never merged: https://github.com/ml-struct-bio/cryodrgn/tree/vb/imagesource-nopreprocess