Some folders may be excluded from version control. It is already possible using a property versioning.unversionedFolders or setting a preference key unversionedFolders.
Some folders are excluded implicitly, for example NetBeans userdir (bug #195284, #195274). Currently the code handling these exceptions resides in the versioning.utils module, i intend to move it to the versioning module for the following reasons:
1) see bug #199951 - versioning module itself needs access to the excluded folders and skip the whole logic in org.netbeans.modules.versioning.VersioningManager.getOwner (the proper fix for the bug). We could either duplicate the code handling the exclusions or move it directly to the proper module and enrich the API. The latter makes more sense IMO.
2) this could limit the number of loaded classes. No implementation of a version control system would be loaded for such folders. For example the mercurial subsystem would not wake up if you ran 'ant tryme' on a netbeans clone (bug #195274) or ran any junit tests with unversionedFolders set to the netbeans clone root folder (currently the switch removes junit workdirs from mercurial version control but the tests still end up loading mercurial classes).