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Right now, regardless of what you type into .cvsignore, NetBean's project files (build.xml include the entire nbproject directory) is checked into CVS either on initial import or subsequent followups when separate project and source directories are not use (e.g. the source directory exists somewhere under the project directory). I brought this up on the nbdev list and Tom Ball asked me to submit a request here. While the intent of the team is fairly clear why they would want to force these atrifacts checked into source control, it is obnoxious to other's that are not using NetBeans or using an old version of it. As Tom pointed out the IDE's job is to be an assistant and not force choices on you.
I'm going to close this as invalid as most folks on the mailing list didn't want this, and simply creating the project directory away from the code directory is a nice workaround. There are other minor issues related to this, but not a big deal as I don't think this will likely be addressed until more folks wanted it anyway.
Reopening, it seems when you split the Project and Source directories of a project, and then "check" the project in, all that gets check in is the empty nbproject directory, none of the source files. So again, there seems no way to import a project into CVS without NetBeans forcing the project files in.
*** This issue has been marked as a duplicate of 72858 ***