Originally posted by Mel Spektor
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There'll still be issues with (overly) complex applications like Visual Studio that do a lot of native interop, or things with C++/CLI. Once again that's because of an incomplete Wine implementation of Windows libraries and functions. But vanilla .NET console and WinForms apps tend to work fine through wine.
The good news is .NET Core makes cross platform much better. But that won't fix programs compiled for .NET Framework. On the other hand, for most simple apps rebuilding it isn't hard, and if it's not obfuscated, an enterprising user can go about rebuilding it themselves since it's all in IL.
As far as UWP, that's not based on .NET. It's an evolution of WinRT stuff, and is callable from .NET and C++. It's just another win32 framework with .NET headers.
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