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Scenario - I have 2 packages pkg1 & pkg2 under src folder - I define src as my source code folder (and give it the label xyz) in project properties and set includes filter for pkg1 only If I now try project->cvs->show changes on 1)my project in the project tab, 2)the src folder label (xyz), the IDE shows me the files from both pkg1 and pkg2 in the cvs window. If I cvs->show changes on the package itself, it shows changes from pkg1 only as expected. I would expect the search for changes to take into consideration the includes/excludes filters that were set.
I checked with standard java projects and exlusions seem to have no affect on Project SourceGroups, ie. in your case sg.contains(pkg2) still returns true. Reassigning to java prioject for evaluation.
The SourceGroup implementation created by SourcesHelper works fine it's even covered by unit test: ant/freeform/test/unit/src/org/netbeans/modules/ant/freeform/FreeformSourcesTest.java. The possible problem is that J2SESources does not listen on changes of INCLUDES, EXCLUDES properties.
Probably the VCS integration is looking at the GENERIC source group, which currently does not do excludes. *** This issue has been marked as a duplicate of 102468 ***