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From the NB CVS documentation, CVS- > Checkout appears to run in the background: cvs checkout -P -R -A -d mySandBox project1/commercial/customerA/moduleX This will checkout the moduleX code into: mySandBox/project1/commercial/customerA/moduleX When issuing the above cvs command on the command line, I will checkout the moduleX code into mySandBox/ I suspect therefor that the NB CVS plugin is actually creating subdirs, prior to issuing the checkout command. This should be an option in the UI, and not done automatically. It's a pain to have to traverse through the subdirs.