Our DVCS team at Intland looked into EGit performance optimization opportunities, and managed to achieve some impressive results! We wanted to share the results with you, so that you don't have to wait for the next official EGit release.
In our optimized plugin version, the time required to synchronize a medium sized repo dropped from 10 minutes to 15 seconds. (It is 40 times faster now on that particular repository.)
The Eclipse CDT team reported similar results: their synchronization time dropped from 32 minutes to 1.5 minutes (roughly 20 times faster now).
Unfortunately this patch you contributed  broke some of the synchronize functionality so we had to revert it . In the meantime we found better ways to improve synchronize performance  and Dariusz is working on some more to come soon.