Make upload/download progress bars more readable

* Add thousands separators to the byte sizes.
* Format the upload and download messages in the same way.
Fix typo
Use traceback.format_exception_only to print error messages

Also, these errors are now printed on stderr rather than stdout.
PTFM-12607: adding bash helper variables

Summary:
1. Refactoring of code, so as to achieve sharing, between local and remote execution.
2. Adding several bash variables available to the application: filenames, prefixes, and paths.
3. Reducing the number of file uploads, to reduce runtime
4. Marking tests correctly, so as not to run jobs

Test Plan: application tests

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D140
PTFM-13510: Making the deepdirs test less fragile

Summary: Simplifying script a little, by avoiding pushd/popd. This seems to fix running on jenkins.

Test Plan: This is an existing test.

Reviewers: bagee

Reviewed By: bagee

Differential Revision: https://phabricator.dnanexus.com/D144
Remove experimental statement from dx-print-bash-vars
'dx cp' regression tests

Summary: Add regression tests for b4d0a74f as well as for other, pre-existing "dx cp" functionality.

Test Plan: This revision contains only test changes

Reviewers: psung

Reviewed By: psung

Subscribers: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D137
PTFM-12428 Remove printing of stack trace for "dx run --ssh" when user's account not configured for SSH.

Summary: Additionally allow specifying DX_USER_CONF_DIR to override ~/.dnanexus_config (affects ../dxpy/scripts/dx.py: ssh_config and verify_ssh_config).

Test Plan: ./test_dxclient.py TestDXClientRun.test_dx_run_ssh_no_config

Reviewers: psung

Reviewed By: psung

Differential Revision: https://phabricator.dnanexus.com/D143
Changelog and version updates for v0.123.0