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FileZilla is the de-facto standard when it comes to an FTP client. It is extremely powerful while remaining very easy to use. You mentioned the user interface, and you're really not going to...
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The standard "Backups" program in Ubuntu will do just fine. It is based on Deja-Dup. It should work with any NAS, since they almost all offer one kind of a networked file system or another...
There is no indication that Ubuntu has stopped providing support and backport updates for JDK6.
As of March 5 2013, Ubuntu was still sending out I don't believe this is possible. By the very nature of what you are doing "switching user" you are effectively logging out to transition from an environment with differing permissions...