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Refactoring how the Scanner system works
It's much simpler: Sphinx finds all files in the given directory, recursively, that have the .rst file extension. And it parses all of them. There is no need to follow "dependencies" to find more things to parse: just parse all files you find. Sure, then later you might be able to give a warning if some documents you rendered were not included in any toctree's - but you will still render those orphan documents.
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