I don't keep very many books on my Kindle. I keep a permanent backup on a USB drive and there they are organized into folders just the way I want them. I also created a spreadsheet with names/authors/source/price/genre and just about any other metadata I could think of. Of course, my spreadsheet indexes into my folder system so I can find any book I want fairly quickly. I put the books I think I'm going to read soon onto the Kindle. If I'm not happy with what's on the Kindle, I can just connect it up to my laptop and transfer any book from the USB drive over to it.
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