Jeremy,
If you didn’t want to check this into CVS then on your intial import it is suggested that you add this to your .cvsignore file. Removing something from CVS that is already in is a PIA, it would require you to:
1) Erase .myeclipse, and resync project, commiting the deletion
2) Add a .cvsignore file with the line “.myeclipse” in it
3) Readd the dir
NOTE: I am not suggesting you do this because step #1 will cause MyEclipse to barf, it needs that directory.
What I would suggest you do at this point is disconnect the project from CVS, go erase it off the CVS server, re-share the project to CVS and on initial import remember to add all the files you don’t want in CVS to .cvsignore.
PLEASE have a sys admin help you with the “Erase from CVS” Step if you have never done it, CVS is a moody system that likes to give unexperienced users such hard times if you manhandle it and I don’t know your level of farmiliarity with admining a CVS install, so I don’t want to give you instructions that shut you down for a few days.