refactor so directories are in order

[MikeLippincott]

          This comment applies to the directory containing this file. Consider continuing the numbering used here and for the `MLP_Model` for other directories in this repository to keep folders organized using numbers. Alternatively, as a larger effort (possibly outside the bounds of this PR), consider using a workflow engine of some kind to help programmatically declare the sequence how directories, notebooks, modules, etc. are used.

Originally posted by @d33bs in #25 (comment)