PubmedArticleDeposit and PubRouterDeposit, clean tmp folder

[gnott]

Stemming from issue https://github.com/elifesciences/issues/issues/4978, there are a couple activities that after they are completed do not delete the files from the temp directory on disk.

These look to be at least the PubmedArticleDeposit and the PubRouterDeposit activities.

The changes should be simple enough:

• At the end of do_activity() of these, clean out the temp directory files using existing code patterns
• Test and fix any test cases that fail due to the clearing away of file artefacts prior to making test assertions