I use Calibre to archive and keep my database as a master but then use send-to-kindle to actually transfer my books to my Kindle. I'm done with side loading and cables and the need for a computer in order to do so.
As to sending personal documents to Amazon, I don't know what kind of documents you people are reading but mine are strictly fiction best-seller books and I could care less if Amazon knows what I'm reading or not so that is why I am OK with send-to-kindle service.
Like a year ago or something like that, send-to-kindle had awful epub to Kindle conversion with send-to-kindle but it seems they have done some work now and my books look really good, just as good as with Calibre conversion. Earlier I was stuck with side loading but now I just can't imagine going back to playing around with cables and laptops in order to transfer book to my Kindle or any e-reader for that matter.
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