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The app.config file is treated specially by the build system and this is not reflected in the Properties panel. It merely indicates that the "Build Action" is None and "Copy to output directory" is "Do not copy". In fact the file _is_ copied to the output directory and is renamed $(TargetName).exe.config. Also, if either "Build Action" or "Copy to Output Directory" you break this behavior. This behavior is "magical" and confusing, especially if you are not familiar with Visual Studio or .NET.
Suggested fix: a special Build Action call "Configuration" that disables other options and reflects this special processing.
I agree it is a bit confusing, but unfortunately we can't change this behavior since it would break compatibility with Visual Studio.