The only ways I know of in the current calibre release for the "deleted" temporary folder to be left behind after you quit calibre is if you quit while that folder was being moved to the recycle bin, and if you do so, calibre pops up a message warning you about it.
Or of course, if something like dropbox blocks calibre from moving the files to the recycle bin. However that should only happen on windows, not linux.
Last edited by kovidgoyal; 11-14-2013 at 02:04 AM.
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