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Do you still include them in the manifest itself with the href pointing into METAINF under a different media-type or just not mention they are there at all in the OPF?
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No, I just don't mention the .wasm file anywhere; I only incluye the proper path to pattern files (.wasm) in Hyphenoly_loader.js. By doing so, as I said, Sigil doesn't report warning or errors and epubcheck accepts the epubs as correct.
By the way, under Sigil Hyphenopoly doesn't work (it has issues with the fetch api) but it works fine with ereaders.