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 think we should maintain module-specific logging folders because there are other modules for the ephemerides pipeline that do require logging. But, I'll accept your recommendation that the logging module automatically create the output folder if it doesn't exist, just make sure to correctly update the permissions after creating it.