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A difference I did notice is that you now must use the
#pragma comment(lib, "libname")
to include any library else linker will fail. That's probably what's messing you up
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You can specify the libraries to use in the linker configuration tab. See the attachment.
And as FEARHQ already said, VC++ .NET can produce native win32 apps. Of course this depends on which components you install. If you only install Visual C# or Visual Basic .Net you can only produce .NET apps
In VS .NET they also updated MFC from 4.x to 7.x.. 7.x for instance supports HTML dialogs.
The debugger was improved. DLL debugging has become a bit easier.
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Also is there any commands to add or omit to make it compile most like VS 6 and less for .NET Standards. A lot of my code that worked before now no longer works with .NET 2003.
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To make your code compatible at first you should look what problems the compiler/linker has (e.g. are there libraries/header files missing, does the compiler have problems with certain expressions, ....). Missing libraries/header files can possibly be fixed in short time. Same goes for certain errors during compilation. Anyways if you get errors like INTERNAL COMPILER ERROR or sth it can get a bit more complicated.