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I'm not sure if you already have a request for this but... It would be nice if Eclipse could have finer grained workspace locking. Even at the project level would be a big improvement as this would allow users to perform, for example, team operations on one project but continue to work on another while the operation completes in the background (i.e. separate thread) (see bug 34906).
Not planning on introducing finer grained locks because this is deadlock prone. Resource scheduling rules can now be used for locking finer-grained portions of the workspace in a deadlock-safe manner. Resource scheduling rules are currently in branch "Bug_36957" but should soon be migrating to HEAD.