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Let me try to briefly answer your first question. Calibre's design requires that books added to its database be copied over into the Calibre folder. That was a design choice made when the program was first created. The Calibre database looks to the folder in which Calibre has stored the book files in order to perform operations and to link the metadata from the database. There have been occasional discussions about this design choice, but it pretty much locked in and isn't going to change.
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