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Calibre stores all ebooks in a specific file structure (by author then by title - it will not be changed, don't bother asking).
However, you can display and find your ebooks in any manner you like. You can change the order of the columns, hide columns, create custom columns and much more. If you can't do what you want with the list, you can probably do it with a custom search. All of this does require learning calibre though - which takes some effort. There are a lot of features in the program.
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