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If I understand you correctly, I think that a good example of a program that provides this feature is Zoot. In Zoot this is simply called inheritence. There is an option on the folder properties dialog that allows you to select inheritence... and when you do, any items that appear in sub folders will also appear in this root folder. It is, indeed, very handy. I don't think it has an option to selectively exempt sub items from being inherited, however.
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