Upgrade to latest cwltool version

[mr-c]

reanahub/reana-commons#427

$ git diff 3.1.20210628163208...3.1.20230719185429 -- cwltool/*.py | diffstat 
 __init__.py              |    1 
 argparser.py             |  254 ++++++++++++++++++++++++++++++++++++++++++++++++++------------------
 builder.py               |  359 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++-----------------------------------------
 checker.py               |  218 ++++++++++++++++++++++++++++++++++++++++++++---------------
 command_line_tool.py     |  729 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-----------------------------------------------------------------------------
 context.py               |  264 ++++++++++++++++++++++++++++++++++++++++++-----------------------------
 cuda.py                  |   67 ++++++++++++++++++
 cwlrdf.py                |  113 +++++++++++++++++-------------
 cwlviewer.py             |  145 ++++++++++++++++++++++-----------------
 docker.py                |  124 +++++++++++++++++++--------------
 docker_id.py             |   10 +-
 env_to_stdout.py         |   10 +-
 errors.py                |    4 -
 executors.py             |  160 ++++++++++++++++---------------------------
 factory.py               |   14 ++-
 job.py                   |  328 ++++++++++++++++++++++++++++++++++++++++++++---------------------------------------------
 load_tool.py             |  285 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------
 loghandler.py            |   29 +++++++
 main.py                  |  632 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-------------------------------------------------------------------------------
 mpi.py                   |    6 -
 mutation.py              |    6 -
 pack.py                  |   99 ++++++++++++++++----------
 pathmapper.py            |   64 +++++++++++++----
 process.py               |  469 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++------------------------------------------------------------
 procgenerator.py         |   16 +---
 resolver.py              |   24 ++----
 run_job.py               |    6 -
 secrets.py               |    2 
 singularity.py           |  272 +++++++++++++++++++++++++++++++++++++++++--------------------------------
 singularity_utils.py     |   30 ++++++++
 software_requirements.py |   55 ++++++++------
 stdfsaccess.py           |    9 --
 subgraph.py              |  164 ++++++++++++++++++++++++++++++--------------
 task_queue.py            |   11 --
 udocker.py               |   10 --
 update.py                |   76 +++++++++-----------
 utils.py                 |  165 +++++++++++++++++++++++++++-----------------
 validate_js.py           |   94 +++++++++++++------------
 workflow.py              |  116 +++++++++++++++++++------------
 workflow_job.py          |  391 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------------
 40 files changed, 3536 insertions(+), 2295 deletions(-)