We've just switched to Git and are trying to find a decent workflow as we had with Subversion. There are a lot of people that were relying on the synchronize view and as it still offers a view on files that might end up with a conflict, they are tempted to use the Merge/Mark as Merged (in git?)/Overwrite in the mouse menu or the icon 'Merge all non-conflicting changes'. When any of these are triggered it seems to break the working copy. Are we doing something wrong here?
I can understand that Git works differently and provides different perspectives and views. But when opening the Git Perspective, the synchronize is there to use. If it provides buttons or menus that conflict with Git, they shouldn't be there. So is this just a bug in showing the wrong buttons/menus or is the functionality behind them buggy? Or might it be that it does work, but not in the expected way?
It would be nice to know the intended semantics of these toolbar items and when they're appropriate to use in EGit. As you point out, their behavior seems wrong in general.
For now I recommend avoiding them, and in fact avoiding the Synchronization view for anything other than the "advanced" version that presents the differences between the active branch and some other branch, tag or reference. This works pretty well and can display the diffs either per commit or per file directory.
To get a summary of the diffs of your working tree v the HEAD or Index, the Git Staging seems like a better choice.