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It is quite confusing in the docs to learn about a Cli-Tool and an Extension, which seem to have different outputs (incl. contained information), config files, and maybe also way of tagging stuff in the source code (marked RST, need refs, one line comment).
As the name of this project is "Sphinx-Codelinks", its focus should be the way how to use it during a Sphinx build, and especially don't explain any config/features which are not integrated into the Sphinx workflow.
I would separate these two tools and have a Cli-Package and a Sphinx-Extension package, which depends on the cli-package.
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