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I see that everytime I perform a pull a full reindex of the repository is performed. This is terribly inefficient with large repositories like mine and leads to a sluggish Eclipse for a minute or two. I have pull set up to rebase automatically, if that makes a difference. I think that the pull operation should use the information on what has changed and only refresh the changed resources. Running Eclipse EGit 3.0.0.201305080800-m7 on Eclipse Kepler, Linux x86_64.
Rebase or not is not relevant. It's laziness on our side. All modifying commands in JGit needs to export information out what files and directories have changed. It is not just pull.