If my reading is correct it seems that the .Net Native compilation is automagically enabled MSDN - Getting Started with .NET Native. I see that it may apply to newly created Windows Store Apps but I am also curious to previously created Store Apps that were created in my Windows 8.1 prior to upgrading to Windows 10. It's confusing because Visual Studio 2013 allowed you to enable this feature and I currently do not see it even after creating a new application.
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It was never part of VS2013, you probably tinkered with the Preview that was released a year ago. It is applied by the Store server, only on apps that target 10. On VS2015 it is automagically enabled on the Release build so that you can verify that it doesn't cause your app to explode. – Hans Passant Jun 11 '15 at 15:15
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Thanks Hans, much appreciated, I'll be validating that is the correct experience tonight. I may have meant VS 2014 and not VS 2013. – Sivx Jun 12 '15 at 17:08
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Unni discussed the use of .Net Native in his build session Deep Dive into XAML and .NET Universal Windows App Development
From slide 9:
All Universal Windows 10 .Net apps delivered to consumer devices will be compiled with .Net Native
Windows 8.1 apps aren't automatically delivered as .Net native.

Rob Caplan - MSFT
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I verified that I was successfully able to produce a Native package. :) Which my main goal was to add some level of **obfuscation** and it worked like a charm. Thanks! – Sivx Jun 15 '15 at 14:02
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'They have to be specifically uploaded as such if desired.' This is not correct. From slide 14: 'Store will reject .NET Native package submissions'. – Alberto Rivelli Jul 17 '15 at 06:29
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@Sivx What did you do with the package? are you sideloading your app? – Alberto Rivelli Jul 17 '15 at 06:38