I keep my books in folders relating to where I got them from (feedbooks/guternburg etc). This makes it a bit easier to process them in a batch if I need to e.g. fiddle with the css. I don't have any shelves, though I will sometimes make one to flag a book in a certain way, say if I have downloaded the wrong language or something. I have a script that generates cover images based on the old penguin covers for each book and copies them into the images folder on the kobo which makes everything nice and uniform. Though I have just started renaming files to kepub.epub to get rid of the long paragraph bug, so it looks like I will need to find another way of doing that (I have around 900 books and don't want to sort the covers out individually).
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