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I think the setup journey and compatibility of wasm still isn't great after all these years. There is still no standard way to handle wasm files across bundlers to my knowledge...
If you are worried about bundling or serving multiple files, perhaps you can just use -sSINGLE_FILE to embed the Wasm code into the JavaScript (avoiding the second file).
If you think there are users out there who cannot switch to WebAssembly, perhaps you could post on emscripten-core/emscripten#27608, and perhaps we could try to find one or two concrete examples, so we can help understand what is holding them back.
We are proposing to remove wasm2js support upstream in emscripten: emscripten-core/emscripten#27608
Would remove that asm.js targets from sql-js be possible at this point?
(emscripten already does not support browsers that pre-date wasm support).