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Synchronize with Repository is a great way to quickly view outgoing changes in the Synchronize view. Currently it requires navigating several levels of a tree and selection of a branch. I always choose the active branch since that's what I am currently working on. To make the Synchronize view more accessible I would suggest adding an item to the top-level repository menu that synchronizes the checked out branch.
Pushed http://egit.eclipse.org/r/4068
Isn't this fixed since a long time? At least I do not have to choose any branch when doing "Synchronize Workspace" in the right-click context menu of projects.