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When Netbeans 6.5 come up and displays currently defined projects, backed by the CVS, nbproject/project.xml is always been marked as changed, and the projects become marked as containing changed files, while the file itself has not been changed by the IDE. Applying CVS diff through the GUI fixes the problem.
The problem occurs with C++ projects; the component "cvs" is described as javacvs, but, as there is no separated C++ CVS component, it look like the "cvs" component is the closest one.