I'd agree to that, but we could also do it at installer runtime, i.e. we check in the Windows SetRegistryKey function(don't know the real name) if the key is autostart related, interupt the installer program and ask the user if he wants to allow that. The method of asking the user at RunOnce has IMO the disadvantage that the user may not know what installer added the RunOnce entry anymore (because it's a couple of days ago that the last Wine instance was running or so).
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