Errors need to interrupt application

[SolomonShorser-OICR]

During a recent run of DownloadDirectory in Jenkins, two steps failed: models2pathsways, and GOAnnotationFile. Both ended in error but the main DownloadDirectory "step" in Jenkins completed.

1. Errors should terminate the main program, rather than be suppressed.
2. Really, each "step" within the DownloadDirectory program should be its own Jenkins step.That way if one fails, the others are not affected.

[cookersjs]

This is still a holdover from running the release by directly calling the DownloadDirectory jar file that allowed all steps to run without terminating if one failed. This will be adjusted so that in Jenkins it is actually terminated -- maybe once it gets to the stage to output which steps had errors, it will throw an error instead of running to completion

[SolomonShorser-OICR]

Jenkins can run steps in parallel. I think the optimal solution would be to have Jenkins run as many different DownloadDirectory "steps" in parallel as possible. If one of them fails, only that would should be re-executed using "restart from stage", or by commenting out the others in the Jenkinsfile.