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Correct. Now that you've pointed out that there are options under Save to disk, I'll be using "Save only EPUB format to disk in a single directory." and deleting the two extra files that appear, rather than having to go into the two layers of folders each time.
I don't use Calibre for the library, just to permanently change an epub title and save it to my downloads folder on my MacBook Pro, and move it from there into my own library folder, where I add aliases if needed (I download lots of history books, so like having the aliases as cross-references). I usually then Airdrop books to my iPad for reading.
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