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That's one of the things Wayland was designed to do, of course implementations can build other things around it that allow privileged clients to break client isolation. The effort could have been put into X11 but it seems the people interested in this would rather put that effort into Wayland.

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That's literally the essence of the CADT[1] model of software development. Why do a comparatively-small amount of unglamorous work to solve a bug when you can just burn everything down and rewrite it from scratch?

[1] https://www.jwz.org/doc/cadt.html

Not really, it's the same amount of work either way considering this doesn't exist yet.

Option 1: add an X extension that lets you configure which windows get to see which input events. Most clients don't actually need to see any events besides the ones they would see while in focus, so most clients don't notice.

Option 2: replace X with something entirely different -- different rendering, different input, different IPC, different organizing principles, different programming models -- and patch all downstream dependencies to use it.

If you can't see that Option 2 is clearly more work and more disruptive, I don't know what else to say to you.

That's not really a reasonable comparison here, because option 2 has already mostly been done, for other reasons.

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