Papers have multiple JATS files

These papers have two JATS files, one in the root, and another in `paper.jats` - https://github.com/openjournals/joss-papers/blob/master/joss.05744 - https://github.com/openjournals/joss-papers/blob/master/joss.05253 - https://github.com/openjournals/joss-papers/blob/master/joss.06415 All incorrectly link to media files that were not moved from the `media` directory.