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What some people do anyway if they will be using Dropbox with calibre, is mirror their calibre library with a one-way sync, using something like linux's rsync or Windows programs like FreeFileSync or DeltaCopy. This prevents Dropbox changes from accidentally clobbering your library, since the master folder never gets touched.
A benefit here is that you can exclude *.azw3 from the mirror.
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Thanks, this actually sounds like a good idea. It'd just be nice if it were built-in, since those azw3s will still be taking up space. Sure this can go around forever: use some script or external tool to remove the azw3 files, and so on. I'm still interested in looking into implementing this but I'd rather not do it if it's not something that would be welcome into Calibre. I guess I'll post to the bug tracker about it.
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You can pause Dropbox syncing and I highly recommend that you do while working in Calibre. To pause Dropbox simply click on the little icon in your system tray, then click the gear at the top right of the menu that appears. One of the options is to pause syncing. Follow the same steps to resume syncing.
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I'm well aware that you can pause dropbox' syncing. I was referring to a feature for specifying a filter/patterns to exclude from the syncing, which dropbox doesn't have as far as I know.