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At the moment, when I right click a project in Eclipse and select 'Synchronize' I get the SelectSynchronizeResourceDialog to poup and ask me for source and destination information. These fields should be populated with sane defaults like the local repository and the current branch. The destination should be most likely origin/master.
Maybe the better approach for this problem would be having two synchronize actions. The first one would be called 'Synchronize' and would perform synchronization operation for current HEAD and origin/master (including local changes). Second one would be 'Synchronize with...' and here we would have SelectSynchronizeResourceDialog ideally with saved last chosen configuration. This approach is more complicated but IMHO it would be more user friendly.
Well we can start with the dialog having sane defaults for now. I'm not sure about taking up menu space with another synchronize related item. The menu is already getting busy :)
Wheel we can discuss how we could reorganize 'Team' menu entry. But for now we can just preset default values as you suggested. Here is a change set for this: http://egit.eclipse.org/r/1321
merged as ad9304982526131ba7664a75dc581360248000a4