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In Windows 8, if a desktop app pops up a notification in the system tray, or flashes its title bar, I don't see any notification of this at all if I'm in a modern-style app! Is there any way to enable notifications for these events?

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No, this is not possible as this is a different environment, so the only solution is using a sound alert which you can hear despites being in the desktop. A lot of applications were warning you is critical have some way to play a sound, if they don't have that (in case of some kind of batch program (like converting media) you might be able to add a line in your batch script that plays a sound; for instance, with VLC player as that has command lines where you can shutdown VLC after you ran it. Otherwise you might just want to regularly check if you got a notification.

If you can get a second screen, that might be handy to put your desktop on while keeping the Modern UI on the other. Which solves your problem altogether if you can afford it.

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Snap might also help in viewing both Desktop and Metro apps together, but of course is quite limited and won't help with other background apps. –  Karan Oct 29 '12 at 17:27
    
Would it be possible, even in theory, to write an app that monitors the desktop and delivers notifications to the modern UI? Or are they completely segregated? –  ekolis Oct 29 '12 at 23:05
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@ekolis: It's possible if you write both a desktop, modern UI and a service for talking between both. –  Tom Wijsman Oct 29 '12 at 23:07
    
Excellent! Guess I'll have to learn a bit about Windows 8 programming... :) –  ekolis Oct 29 '12 at 23:08
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