I have experienced some issues with Eclipse and EGit.
When I create a new class in my existing repository, it is kind of not linked an changes in this class aren't visible in the unstaged changes in the git view of eclipse.
I have tried to track the new class via the team menu of the right click menu of the class, but didn't find any way of fixing my problem.
I have the latest version of eclipse installed.
The problem was, that the full path of the repository was in the gitignore. Deleted the content of it and everything is back fine.