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Store Code etc for technical books

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I've started using calibre since my library has grown (my books are in a series of different folders but I haven't figured out a good answer of where to store my code as the zip and HTML files are being identified as books when I import my existing files into the calibre library.

I'm thinking perhaps I should move all of the code to a separate folders outside of the folder where I current store my books as I import them into Calibre. Any other strategies or configurable options that you've found?

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