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If there's an existing flake8 check or plugin that does this, it might just be a matter of adding the right incantations so that that check covers stub files.
In typeshed we now get unused import checking from Pyright. I suppose it's still useful for flake8 to do it too (e.g. for other stub projects that don't support Pyright), but it feels low priority.
A check that knows the special import handling in stubs. E.g.:
This should complain about
a
being unused, but notb
orc
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