Make gcp-direct.sh deal properly with the envir...
Changing the order of PRs in an application in the GUI resets the run flag
Point to updated version of the Evaluation plugin.
Correct the zip download URL.
Ontology plugin doesn't always recognize OWL individuals
Improve how urls to resources get stored in a pipeline file
This has been fixed with the fix for issue #201
Filepicker sometimes uses original and sometimes real path