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I only use one function of Calibre, and that is command-line conversion between e-book formats. For many reasons, some of which are:
1) Organizing books via the filesystem is so much faster and more comfortable for me.
2) I am a control freak and I don't want Calibre to clutter my painstakingly cleaned-up e-books with its tags, except when putting them on the reader device. Calibre content is not good enough for storage, as far as I am concerned.
3) I use multiple devices and I want significant customizations on each - but I want one source book so that any found mistakes can be fixed in one place. That can be easily done with my source files and a preprocessor, not so with a third-party tool.
And many more.
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