No matter what I do (Pull, Fetch, Overwrite, Mark as Merged, etc.) the Synchronize view always show differences in the tree on the left. When I open the individual files in the Compare Editor there are no differences in the files. I have tried setting "core.autocrlf=false" in the configuration and re-cloning my repository but to no avail. Some posts on this forum suggests that Synchronize just doesn't work with Git. Has anyone got this working?
If you have command-line Git installed, try running 'git status' on your clone and then refreshing your Eclipse projects. Some side-effect of 'git status' seems to clear these kinds of issues in EGit/JGit.
re: Synchronized view, this is mostly useful when comparing the current HEAD with some other branch. If you want see the status of your working tree and/or Index relative to HEAD, use the 'Git Staging' view.