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The autotools plugin updates make targets by iterating of all targets and making calls to org.eclipse.cdt.make.internal.core.MakeTarget.set* through IMakeTarget several of these calls result in a call to projectTargets.saveTargets(); which again iterates over all targets. This results in an O(n^2) situation casing eclipse to hang. It would be nice if there is an interface to update a MakeTarget without calling save all