Minor test fixes

* Use dxpy instead of shelling out to "dx new project", "dx wait", etc.
  Considering that each setUp and tearDown used to invoke dx twice, this
  should save upwards of 300ms *per test*.
* Convert some print statements to test names.
* assertSubprocessFailure no longer prints out stderr unless the regexp
  assertion failed; it's likely that check_output already printed stderr
  out anyway, so such lines were duplicated.
Fixup bb71c96: use terminateJobs to reproduce original destroy call
Update exec_io.py

Updating to point to new reference genomes project (file based instead of gtable based) and also making sure that the bill-to for the project is org-dnanexus so outside users can't publish a project w/ the same name and have it discovered by dx in place of ours.
Moving options to import reads, mappings, and variants from visible options to hidden.  They're still available, but won't be advertised by the application.
Merge branch 'master' of https://github.com/dnanexus/dx-toolkit
Tweak help message
Fixup for 30994a91: move format_exception to exceptions module
PTFM-13652: improved prefix bash variable

Summary: Added tests, and code, that implements the improved bash prefix variable. It takes patterns into account, and also the '.gz' suffix.

Test Plan: An additional test app, prefix_patterns, was added to the file_load subdirectory.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D148
PTFM-13152 Remove app-specific validations when building applets.

Summary:
Additionally check for existence of applet with same name in
destination before uploading resources when "dx build" not
supplied with "-f" or "-a" flag and add tests for building applets.

Remove do_build_step and do_upload_step from build_and_upload_locally() declaration.

Add lint fixes and minor changes.

Test Plan: ./test_dxclient.py TestDXBuildApp

Reviewers: psung

Reviewed By: psung

Subscribers: psung

Differential Revision: https://phabricator.dnanexus.com/D149
Bash vars bugfix and style improvements
Changelog and version updates for v0.124.0, UA 1.5.5