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've added the module name back into the path, and now the logging path specified in `settings.yaml` as well as the module-specific directory inside it are automatically created if they don't already exist. Their permissions are set to be owner and group writable, readable, and executable, and readable and executable by the world (drwxrwxr-x in fewer words, 775 in even fewer characters, 0775 in python's `chmod` octal).