Functionality update

- Purpose: Functionality of this version of the MFR matches or exceeds functionality of vendorized version in the OSF. This will continue to be developed as external module, vendorized version discarded. 

- Changes: Add support for ipynb, pbd, pdf files. Remove support for extensionless files without explicit action by user to include it.

- Side Effects: fix flake8/testing issues

Progresses: https://github.com/CenterForOpenScience/osf.io/issues/1273