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IResource#setDerived(boolean) is deprecated. New Use IResource#setDerived(boolean, IProgressMonitor) should be use instead which is a workspace operation and generates delta. See bug 45805.
Created attachment 147712 [details] Fix v01
The org.eclipse.jdt.core.tests.performance.FullSourceWorkspaceBuildTests suite doesn't indicate performance regression on my machine. However we would have to run the tests on our build servers to be absolutely sure.
I'll commit the patch.
Released for 3.6M3. This needs code inspection to be verified.
Verified for 3.6 M3 by code inspection