Avoid monkey patching shlex globally (fixes test broken by 49c2bbb)
Build dxpy source distribution and use pip to install from it

This is needed because when using dxpy's "setup.py install", the
resulting installation injects a setuptools path into sys.path before
our own path, causing us to rely on an external pkg_resources file
from setuptools, and if that is too far out of date, it's unable to
resolve newer-format dependencies (ones that use "dist-info"
directories).

In particular, this should resolve the
"pkg_resources.DistributionNotFound: requests==2.3.0" message on
CentOS.
Revert "Build dxpy source distribution and use pip to install from it"

This reverts commit 2563e6091f8653c676ea32db222caa080e817054.
PTFM-13049 Source build venv before installing

This is intended to avoid the use of an out of date
setuptools/distutils when installing dxpy, eliminating errors like
"pkg_resources.DistributionNotFound: requests==2.3.0".
Make test wait for files to close before invoking dx-run-app-locally

While the system waits for files to close before running jobs,
dx-run-app-locally does not.
PTFM-8497: fixes for dx describe jobs with resolved JBORs

Summary:
In particular, use additional API calls to ensure that the correct
resolutions are reported (even in cases of flattened arrays, etc.)

Test Plan: added unit test

Reviewers: akislyuk

Reviewed By: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D80
Remove now-broken test for retrieving resolved JBORs
Changelog and version updates for v0.115.0
PTFM-13049 Inject SDK path into sys.path in Setuptools entry points

Force our Python path to appear before everything else in
sys.path. This is necessary when an out-of-date installation of
Setuptools appears in sys.path, providing a version of
pkg_resources.py that is unable to read our Python package
requirements metadata, and crashes with a
pkg_resources.DistributionNotFound error.
Some line wrapping fixes

Test Plan: existing unit test

Reviewers: akislyuk

Reviewed By: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D84
dx describe bugfix for resolved array indexed JBORs
Test fix (need quotes around JSON string as bash argument)
Fix race condition in test (need to wait for state runnable)
PTFM-13132 Fix dx sh with stdin commands
dx ssh: Use dnanex.us instead of dnanexus.io
Fix dx upload -r x y --dest z
Merge branch 'master' into PTFM-12607-bash-helper-variables