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How do I encrypt but share a number of folders?

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http://askubuntu.com – I want to achieve the following functionality. Is it possible? Boot up computer (possibly via WakeOnLan or WakeOnPlan). Either be automatically logged in, or log in via login screen, or log in remotely. I change this behavior occasionally, so full disk encryption wouldn't work for me because it requires a password on bootup (which would it would prevent the remote bootup options, and the automatic login option). I am only interested in encrypting data, not the entire harddrive. Once logged in either: a launcher/tray icon is available to launch encryption app (preferred) run encryption app (HowTos)