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But now I'm wondering, what location should I be downloading these ebook files to? Should I specify the folder as the root, or instead create a separate downloads folder? Will this interfere with Calibre, or create a problem if I switch back and forth between KOReader and Kobo's software?
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That depends on whether you want Nickel to see it or not. If you don't, put it in a hidden folder, for example .books (note the . at the beginning). If you do, it doesn't matter. I don't think Calibre cares.