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Calibre's default behavior of Sending books to the Kindle will create subfolders based on author/book-title in the documents folder. The Kindle doesn't seem to care about subfolders when showing titles on your Home screen. I don't know if it slows things down or not.
You can stop calibre from creating subfolders (or change the naming scheme) by modifying the Send to preferences and/or the Kindle device driver plugin settings.
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