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It turns out there is a bug in the Castagna paper for BDD difference (confirmed with Castagna) and it is necessary to materialize the unions when the atoms are equal
ballerina-platform/nballerina#757 (comment)
This means fixing #3 by using the formula in the Castagna paper is not the correct fix.
Also worth noting is that your formula for complement is different from the formula in the Frisch PhD thesis. Your one is right, and the thesis one is wrong.
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