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One organizational note that I failed to mention is that I like to keep the originals of all the ebooks that I purchase (or download for the Gutenberg books) in a directory structure separated by where I got them from. Thus for me, I have a directory structure with the root directory being ebooks, then subdirectories for kindle, sony, baen and Gutenberg. I keep that directory tree archived so it's pretty easy to find the original in case of a problem. I also keep my calibre directory structure backed up.
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