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There are two limitations with Java discoverer, when invoking DiscoverJavaModelFromJavaProject from Java in silent mode, in providing some IJavaProject collection as input. if source = projectA, and parameters bean contains projectB and projectC - it does not work for projectA if it is not explicetely added in parameters bean - project B and C are not processed if they do not appear in projectA dependencies These limitations are side-effects from behavior with UI projects selection. But they must not exist.
Fixed in revision 3560.
Bug fixed.