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Is the problem reproduceable in regular Alloy4 itself? If you can capture the intermediate Alloy model that your tool
generates, or capture the intermediate Kodkod input, then we can see if it's reproduceable in regular Alloy4,
and if so, it'll be really easy for me to isolate the problem and also see whether it's a problem in Kodkod or a problem in Alloy4.
(By the way, the Alloy4 and Kodkod source code are directly embedded in the standard Alloy4 download jar,
though it appears they are not included in the standard A4E download)
Sincerely,
Felix Chang