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I want to only sync files with a certain prefix in a folder. Is there some way I can get Ubuntu one to only sync these files or ignore other files?

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At the moment, there's no good way to exclude certain files in certain directories. That said, you can ignore certain file types across the board by specifying regexes in: /etc/xdg/ubuntuone/syncdaemon.conf

See the ignore.default part of it.

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