User data patch

This is a mixed bag of updates and a few fixes. I changed the naming of the parameters for the classes the user works with directly such that these parameters to not start with and underscore, for clarity in the documentatio. Bug fix. The default jobs was not working in all cases.
Bug fix. I reset the index of GeoDataFrames which fixed some issues in some files.

Documentation: Added the classes return from pre-processing function of user data classes.