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Dependency metadata generated for sources bundles includes information from project's p2.inf. This results in sources bundles being selected by dependency resolver instead of their corresponding main bundles in some cases.
Should be fixed now. http://git.eclipse.org/c/tycho/org.eclipse.tycho.git/commit/?id=61745a07839a41c9fcc62e8b1c8701d4a4a2bc22