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Under some timing the up to date check does not process sources. It just does collect project dependencies and up to date check of binaries. It seems as a visibility race.
Fixed jet-main 7f8bd5bd3e30
Integrated into 'main-golden', will be available in build *201204260400* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main-golden/rev/7f8bd5bd3e30 User: Tomas Zezula <tzezula@netbeans.org> Log: #211675:Up to date check sometimes does not proceess source roots.