For your CVS issue, you might try the Filters option on Package Explorer title bar pull down menu (the little down arrow). It has a bunch of options to control the types of resources that display. I have searched my configuration and don't see anything special that I have set up to exclude the CVS files, but they do not show on my system.
I think as long as the project is shared, eclipse won't show .CVS. The only time you'll see them if i'm right is if you check out a project from cvs using a cvs client other than eclipse and create an eclipse project based on those files. Tim, if that's basically how you ended up with your project, you'll probably want to right click on your project, team -> sharing and enter your cvs information or something along those lines.
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