Supporting the -except flag for upload outputs

Summary:
Improving handling of arrays, and adding the --except flag.

Minor fixes

minor fixes

Test Plan: updated unit tests.

Reviewers: psung

Differential Revision: https://phabricator.dnanexus.com/D66
Merge branch 'PTFM-12586-bash-helpers-order-file-array' of github.com:dnanexus/dx-toolkit into PTFM-12586-bash-helpers-order-file-array
Fixing code review