is it intended, that the changes view also lists files, those folders have a CVS-dir but are not part of the module-structure? I got several hundred files under some copied directories which are not accessible via the modules, but lay inside the project root.
I would think, as long as they weren't references in a module, they should not be considered in update and commit operations (like it was the way in IDEA 6, btw.).
Another issue: if there's no CVS-dir under the project root, but only inside the modules beneath, updating the whole project using Ctrl-T does not work. This wasn't the case in IDEA 6 and is very inconvenient.