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If I want to rebase a branch it would feel natural to me to select the branch I want to rebase and trigger the rebase over it's context menu. Sadly I can press rebase on every branch but the current checked out. I think this is very confusing.
It's the other way round : - click "Rebase" on the branch your currently checked out branch should be rebased onto http://wiki.eclipse.org/EGit/User_Guide#Starting_Rebase