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You can organize your files in whatever folder structure you want, but as far as I know Quartus will always show the files flat in the "Files" view of the Project Navigator.
However, did you notice that there's a "Hierarchy" view in the Project Navigator? As soon as you ran synthesis (or at least analysis & elaboration), it'll show you a hierarchical view of the source files. I know this is not exactly what you asked for, but the closes Quartus feature I know of.
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The hierarchy view is not of the source files; it's the hierarchical view of the design entities and their instantiations after analysis & elaboration. In the Files view of the project navigator, you can see all the files used by the compiler, but they are not organized hierarchically.
Honored Contributor
