Merging the use of num_cores in settings.yaml

Ticket #130  describes the changes I've made in this branch. I believe it's ready to be merged into `master`.
I described why I think this should be removed in Ticket #130:

I've gotten rid of `module_name` from the logging path, so that the pipeline's logs actually go into the path specified in `settings.yaml`.

If we do implement logging for the other modules, we could put the module name back in the path. But at the moment, the pipeline fails to run if the user doesn't beforehand manually create a `run_imaging_pipeline` directory inside the directory specified by `logging_path`, which they had no way of knowing they needed to do. If we want to add module-specific logging, we should at least have the pipeline automatically create those folders.