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This is actually a regression. There is not implemented annotation of data objects that have more then one file.
Fixed in trunk: /cvs/vcscore/src/org/netbeans/modules/vcscore/VcsFileSystem.java,v <-- VcsFileSystem.java new revision: 1.320; previous revision: 1.319 /cvs/vcscore/src/org/netbeans/modules/vcscore/caching/StatusFormat.java,v <-- StatusFormat.java new revision: 1.11; previous revision: 1.10