PTFM-7006 Adding bash helpers for upload/download of multiple files.

Summary:
These are implemented as python scripts, called dx-upload-all-outputs, dx-download-all-inputs,
dx-download-input.

Test Plan: Added unit tests that work locally, written in python.

Reviewers: klai

Differential Revision: https://phabricator.dnanexus.com/D19
Merge branch 'ptfm-7006-bash-util' of github.com:dnanexus/dx-toolkit into ptfm-7006-bash-util
Fixed the comments on documentation