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Every single time I try to open a PDF with Sioyek from terminal (using open command) I get this annoying warning:

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Is there anyway to get rid of this? Ideally I don't want macOS to ever warn me about this.

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At a guess, by opening it from Terminal, you're bypassing the Quarantine requirement.

Try opening the app once from Finder, by right click, Open - then confirm the dialog. Then test Terminal again.

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