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In order to keep certain settings in sync, is it a good idea to place app configuration files into ~/Ubuntu One folder, e.g. ~/Ubuntu One/.myapp/myapp.conf?

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I'd suggest making hard links to ~/Ubuntu One instead of placing the actual files. – Adobe Jul 7 '12 at 8:35
Doesn't Ubuntu One replace files when it gets new versions? I've been placing the real config file in there, and using soft links in the place where the application expects it's config to be. – Adrian Jul 7 '12 at 19:34
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See Will Ubuntu One support OS Settings sync? for some discussion on this point. In general, as dobey says above, it's not a good idea to sync configuration files for apps, because the apps are not written with the expectation that those files might change. To sync app settings, you really need cooperation from the apps.

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Generally, no, it's not a good idea to store configuration files in Ubuntu One. There was a session at UDS Q about this. I'm not sure where the audio stream is for that at the moment, or the Etherpad URL, but it's worth going through.

Most applications do not do the right thing with storing settings (configuration/preferences), state, and authentication details, and will often lump them all together. Also, even if all the apps did do this correctly, using Ubuntu One file synchronization is the wrong way to go about syncing such data. The upcoming u1db structured data storage and synchronization support, would be a much better way of doing the job.

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