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If you really, really want your Calibre folders to group by genre *and* you don't mind using Calibre in non-standard ways:
*use the Author/Author Sort fields for Genre
*but the author name in the tags field or in a custom column
This wouldn't give you folders grouped by author within your genre folders, though. You could experiment with combining genre and author in the author/author sort fields, I suppose.
Officially, itimpi has the best answer for the way Calibre was designed to be used. You're supposed to use the Calibre interface to access those folders - you're NOT supposed to go into them directly using whatever file manager program you use.
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