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We already have a similar and much more detailed section in howto.rst. Further, the included run.py usage print will often be out-of-date and manually updating it every time isn't maintainable.

To manage external links such as for Python Modules, we are now using the extension sphinx.ext.extlinks to define all of them in the file doc/external_links.py.

Also adding some labels needed for referencing various parts of the
rest of the documentation.