CWL:fix support for user space overrides

[mr-c]

Actual fix for #2333

[cgcloud-jenkins]

Build finished. 18 tests run, 0 skipped, 0 failed.

[cgcloud-jenkins]

Build finished. 885 tests run, 39 skipped, 3 failed.

[DailyDreaming]

The failing cwl tests: http://jenkins.cgcloud.info/job/toil-pull-requests/4321/

[mr-c]

Thank you @DailyDreaming ; turns out that cwltool didn't have its own tests for the bioconda/biocontainers feature! That failure has been fixed via common-workflow-language/cwltool#874

[mr-c]

@DailyDreaming Looks like the Jenkins-cgcloud-github account also needs its permission adjusted?

Using context: jenkins-it
FileNotFoundException means that the credentials Jenkins is using is probably wrong. Or the user account does not have write access to the repo.
org.kohsuke.github.GHFileNotFoundException: {"message":"Not Found","documentation_url":"https://developer.github.com/v3/repos/statuses/#create-a-status"}

http://jenkins.cgcloud.info/job/toil-pull-request-integration-tests/2612/console

[cgcloud-jenkins]

Build finished. 18 tests run, 0 skipped, 0 failed.

[DailyDreaming]

@mr-c Will check on that!

[cgcloud-jenkins]

Build finished. 885 tests run, 39 skipped, 2 failed.

[DailyDreaming]

@mr-c Yes, the permissions need adjusting, but the global jenkins settings need to switch to DataBiosphere, while there are still projects in bd2k that would break if we did that, so we need to separate those two. Will fix that soon, though other things (like the mesos refactor) are higher on the priority list right now.

[cgcloud-jenkins]

Build finished. No test results found.

[cgcloud-jenkins]

Build finished. No test results found.

[mr-c]

Jenkins, test this please

[cgcloud-jenkins]

Build finished. No test results found.

[cgcloud-jenkins]

Build finished. 18 tests run, 0 skipped, 0 failed.

[DailyDreaming]

No matching distribution found for cwltool==1.0.20180820141117

http://jenkins.cgcloud.info/job/toil-pull-requests/4329/console

[mr-c]

Jenkins, test this please

[cgcloud-jenkins]

Build finished. 18 tests run, 0 skipped, 0 failed.

[cgcloud-jenkins]

Build finished. 885 tests run, 39 skipped, 0 failed.

[DailyDreaming]

@mr-c This looks great. Thanks for the additional refactor/naming too, much appreciated.