An improved dx-upload-all script that knows how to upload subdirectories
from the job's output dir to the project space as folders.

Test Plan: added a test called file_test/deepdirs

Reviewers: klai

Differential Revision: https://phabricator.dnanexus.com/D97
Merge branch 'PTFM-12609-allow-subdir-outputs' of github.com:dnanexus/dx-toolkit into PTFM-12609-allow-subdir-outputs