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Using Netbeans 6 Milestone 3 (but also apllies for previous versions) I think Eclipse handles multiple SCM repositories better than Netbans. In Eclipse I don't have a CVS, Subversion or whatever top level menu item. Instead I have a "Team" menu where all the commands are. If my project is from a CVS repo then all the Team commands act as CVS commands, and likewise if my project is subversion based. Looking at the current menus only the tagging and branching item are differntly, all the rest are completly the same. Suggets netbeans start using an approach similar to eclipse.
We now have only one Versioning top level menu that lists appropriate commands based on current context.