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

I assume that `debug` is just for turning on print statements when developing code. We definitely don't want to propagate these sorts of hacks into the Python version, so I think we can safely ignore them.

More generally, I've been trying to limit functionality to just the stuff thats actually used in the script version that we're working on. Otherwise, I'm afraid we'll quickly end up with a codebase that is nearly as spagettified as the Yorick code. This means I have not been trying to implement all the options used anywhere in DDT... just the ones that are used in the script `run_ddt_galaxy_subtraction_all_regul_variable_all_epoch.i` with the example configuration file. 

If you're not yet sure what options are used from that script, its fine to leave them in and add a `# TODO`.