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As has been mentioned, playing around with Calibre's internal folders is normally a very bad idea.
Having said that, the folder structure will reflect how the Author field is set up in Calibre. I set my Author field up as "Firstname Lastname" and thus see that as my folder structure which means it orders on first name. If I had set the author field up in "Lastname, Firstname" format then the folders would have been ordered on Lastname.
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