Add a --multi-hdu option

This writes all the images as multiple HDUs in the same file.
Now PEP 8 compliant
Fixes required by the Keck proplyd project

* spotless.py:

  1. Allow multi-HDU output even when the input file only has one HDU

  2. Raise only a warning, not an error if a non-existent region file is
     specified.

  3. Bad pixels specified via --include-regions-file now override
     everything .