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I use EncFS with Dropbox.

It's an almost completely transparent user-space filesystem. Basically you store your files in a given folder, and it automatically stores a parallel encrypted copy in a different folder.

http://www.howtogeek.com/121737/how-to-encrypt-cloud-storage...

Does it do data deduplication? Doesn't sound like it to me from skimming that article.

Edit: sounds like EncFS has some significant security issues: http://sourceforge.net/p/encfs/mailman/message/31849549/. No recent information in that discussion, so I don't know whether it's all been resolved. Here's an HN discussion of the audit: https://news.ycombinator.com/item?id=7384730

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