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Originally Posted by Worldwalker
Calibre does leave your files where they are. It just makes its own copies ...
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Yes, it does that; your're correct, of course. I'd still be given the option for it not to. Storage space is cheap these days, it's true, but I still see no need to keep those files in duplicate.
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Why do you need to access your ebook files directly?
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My filenames follow a certain naming convention, they include a small taxonomic signature (like Dewey, only totally different). It allows me to quickly find any book I'm looking for; faster even than with a full text search.
But this is probably getting off topic here ...