Decided to follow your suggestion and split it into 2 zips, since bundling the source was leading to other problems!
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I also opened a feature request in the forums asking for some official guidelines, and maybe proper support for pdx.zip (both for tooling and sideloading to the device itself) to ease the process for users. https://devforum.play.date/t/standardize-and-document-way-to-distribute-games-fi...