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I honestly can't contribute information to that. I remember noticing a problem when documenting init_lookup_tables.cpp and creating the diagrams. I think the quark indices simply were in the wrong place. I can easily imagine this problem being automatically cured by the latest refactoring.
Probably it would be the safest to calculate some strange quantiity and check whether all quark exchange symmetries are behaving as they should. As long as only one quark flavor is used, it will always be correct.
In the code which is now refactored away there was a comment by @maowerner:
Is this still an issue?
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