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When I first started using Calibre, I only wanted to use it as a file converter and metadata changer also. I just copied books to it from my personal files and let Calibre create its own set of files for each book. After I fixed the metadata and converted, I'd go to the Calibre folder and move the newly created files over to my personal filing system with all its folders and lovely sub-sub folders. You could do that too.
Then I found I hated the way the Sony software kept crashing and decided to use C exclusively. However, I still keep my personal files separate, and just ignore Calibre's copies. I haven't kept up the copying/moving to the personal files, but I know I could if I wanted to.
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