Patch Set 3:

Interesting, can you try this and let me know if it works for you, Dariusz?

1. Close all projects except 'org.eclipse.jgit' and 'org.eclipse.jgit.console', which should both be version controlled with EGit.
2. Right-click on one of the projects > Team > Synchronize Workspace
3. Open one file from each project and make both editors dirty.
4. Ctrl+Shift+S to save all editors.
5. The refresh(IResource[], int, IProgressMonitor) method should be called with two projects.

Further optimization should be possible by only having the refresh be performed on those two individual files. I think we can have a separate change set centered around GitSubscriberMergeContext (which you were previously working on) for that.