Merge core.py with various ...toolbox...py files

I think we should make an effort to strip out options that may not be used anywhere. For example, I don't think this `galaxy` option is used anywhere in the code base.

In fact, for this function (`calc_residual`), I'd start by only having `ddt` as a parameter. You can always add more options later if you encounter calls to `calc_residual` that actually use the optional functionality.