PTFM-13795 session conf dir cleanup

Reviewed in https://github.com/dnanexus/dx-toolkit/pull/80.
Document the dxpy.utils module.

* Upgrade doc build dependencies
* Fix doc formatting for exec_utils
Changelog and version updates for v0.128.0
Don't print an error when running dx with freshly init'd user config
PTFM-14034 Bump requests dependency from v2.4.3 to v2.5.0

This pulls in an upstream bug fix to handle
OpenSSL.SSL.WantWriteError.
Fixing bash helpers vars test

Summary:
Fixing test app file_load/vars, to properly check for array equivalence. This ensures
correctness of the bash helper variables.

Test Plan: Fixing a test.

Reviewers: klai

Reviewed By: klai

Differential Revision: https://phabricator.dnanexus.com/D150
Lint fixes for cp.py

Summary: Lint fixes for the cli/cp.py file.

Test Plan: Existing test suits

Reviewers: akislyuk

Reviewed By: akislyuk

Differential Revision: https://phabricator.dnanexus.com/D191
PTFM-12058: Remove workaround to re-describe workflows
Fix test_dx_run_debug_on
Unadvertise dx import and new gtable

They still work, just won't be advertised through help or command line
completion.
Add pip back to the list of grouping PMs

This is a short-term fix for an issue with Python packages
that clobber the install environment for other packages.
Fix completion tests after d8408eba
Fix exec depends installer tests after c122acc2
Merge branch 'master' into PTFM-13951-retry-connection-errors