run-workflow: Fix baclava output option.

The description of this option says that the filename is optional, but it
wasn't. Now fixed.
Fix error in exception caused by chunked response.

If there is a chunked response I am not sure how to get any error message out of
the internal Net:: classes. So for now at least cope better with what we get.
Add provenance capture and retrieval functionality.

Can now turn on provenance generation and get a run-bundle once the run has
finished.