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Hsawires,
Calibre's library file structure, as BetterRed posted in message #3, is hard-coded into the program due to various internal functions that need to know exactly where the e-book files can be found. Because of this requirement calibre's library structure cannot and will not be changed. (Kovid has said this repeatedly and there are multiple variants of this conversation available in these forums.)
More importantly, you should not be performing any actions to the calibre library (structure or files) either manually or through any other software. Any manipulation of the files outside of calibre could lead to data loss. Which means, if you don't have a copy of your books elsewhere, either through calibre or a separate backup, you might suffer permanent loss.
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