When you do a Commit, you will see files listed with question marks in from of them. You really need to resolve these files. If you don't you may work on a file for weeks and never add it to the repository. If it is buried in among 30 or 40 question marked files, you could very easily miss it.
You resolve these files in two ways.
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Add them to the repository with a cvs add xxxx.java command.
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Include the file name in a .cvsignore file in the same folder.