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CVS view, right click on cvs project, and select "Check out as..." and click next to choose java project, enter a project name you know you've never had in eclipse ie: yaddayaddayadda, click finish. Doesn't matter what you answer to the confirm perspective switch, immediately after that you will get: The resource "yaddayaddayadda" already exists in the workspace. Overwrite? This should happen, the resource never existed in my workspace until I began the check out process.
This is still occurring, and is VERY annoying whenever you are loading in a new project from CVS, which I do very fairly often.
Unfortunately, this is not as easy to fix as it should be and points to a bigger issue in how projects with a particulr nature are created (e.g java nature). The workaround is to commit the .project to the repository. Hopefully, we will be able to address this properly in 2.2.
Add to readme for 2.1
This was fixed in 3.0 M3