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Feel free to use whatever method you like to store your books. I dont expect calibre to work for everyone. IMO it is the best method to organize an e-book collection of any significant size, but other people can well have different opinions/needs. That is why I have tried to make calibre as modular as possible, with separate executables to run only the viewer, the conversion engine, the editor, etc. So use the parts that make sense for your workflow.
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