DRY: use sphinxcontrib-autoprogram to not repeat CLI option help text

[mr-c]

https://sphinxcontrib-autoprogram.readthedocs.io/en/stable/

Ideally https://github.com/DataBiosphere/toil/blob/master/src/toil/options/common.py would match the content in https://toil.readthedocs.io/en/latest/running/cliOptions.html and

toil/docs/running/cliOptions.rst

Lines 77 to 79 in c7e522d

	Commandline Options
	-------------------

would look like https://github.com/common-workflow-language/cwltool/blob/main/docs/cli.rst?plain=1

• refactor add_logging_options() to return the parser group so that related logging options can be added to that group afterwards by the caller

Example usage in cwltool via https://github.com/common-workflow-language/cwltool/blob/10cabefa0576bc950f6ce1c6f01ab7d3e3357617/cwltool/argparser.py#L57 : https://cwltool.readthedocs.io/en/latest/cli.html

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1827

[mr-c]

This approach also automatically tag the rendered CLI docs with :option: directives, allowing for easier referencing and hyperlinking from other parts of the docs with :option:`--some-toil-flag` .