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

Differential Revision: https://phabricator.dnanexus.com/D144
Setting bash to echo the commands, so we can better figure out what is going on during failure.
Merge branch 'PTFM-13510-deepdirs-fix' of github.com:dnanexus/dx-toolkit into PTFM-13510-deepdirs-fix