Output files documentation

[MikeAxtell]

Hi again Michael. This is comment / enhancement request, not a bug report.

I think that new users would benefit from an expanded README or manual that more clearly explains the contents and meaning of the various output files. Each step in the pipeline creates quite a few output files. I can deduce a lot from the names of these files, but would still benefit from having some of the details more clearly explained.

Thanks for considering!