The repository root directory, IMHO,
should just have module directory names in it, including CVSROOT. Your
root directory looks like it has project stuff mishmashed e.g. source with
CVSROOT and modules . If it were me, I would reorganize the repo
to move all the project related stuff into module subdirectories and checkout
exactly the module tree you need, leaving CVSROOT out of the checkout.
This may help to isolate the project related files you need to 'cvs
add' or whatever which are causing your update message.