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The VCS output is the same kind of beast as any other output and conceptually belongs to the output window. Opening it as a TopComponent on the desktop has several bad usability sideffects, and even if the user docks it into output window herselves, because there are multiple VCS output windows, all new ones keep opening on the desktop. I suggest to create a single VCS Output window, docked as a tab in the output window.
This was already discussed on nbui some time ago. We did not come to a conclusion yet, with Chris we agreed to do it in 4.0 timeframe.
This was already solved in NetBeans 3.6.