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I remember way back when when doing some research into the Win32 API that the function you use to save stuff to the registry had a flag argument that was, essentially, save-to-registry vs. save-to-file. I assume that's gone now?
No. It was never there, sorta-kinda. The function I think you're thinking of is called WritePrivateProfileString, and it's designed for writing to an INI file. You can map writes to particular INI files to the registry (by some settings in the registry).
OTOH, you could be thinking of MFC's CWinApp::WriteProfileString which writes to a file unless you've called CWinApp::SetRegistryKey, in which case it writes to the registry.
But, this is not hugely relevant, because we're talking about .NET, in which, bizarrely, Microsoft left out a configuration API (although, as Andy says, it's in .NET 2.0). Of course, you can call the Win32 API functions via P/Invoke.
Or you could just roll your own. It wouldn't be that hard.
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roger