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I've finally figured out the problem, and posting the answer here to help any who may be interested. The issue turned out to have nothing to do with Micronaut or compatibility issues between Micronaut and Launch4j, but rather a seeming limitation within Launch4j when working with jar files that contain too many files. The migration to Micronaut pushed the number of files beyond the 32-bit jar limit of 65535, necessitating adding the zip64 true flag as seen above. However, once that limit is passed Launch4j breaks, and I wasn't able to find any means of settings an equivalent zip64 flag on it. In fact I found virtually no information in terms of Launch4j file count limitations (so the limi…

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Answer selected by cancech
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