Papers have multiple JATS files

[sneakers-the-rat]

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.