You have carried out a cvs add
on a directory. Even though you have not done a cvs commit
yet, these directories now permanently live in the repository as CVS creates them immediately. Files behave differently - they only get added to the repository on commit.
CVS itself does not offer any ability to remove directories once they have been added. Unless you add and commit the files in the git directory, there will be no further negative consequences to your repository.
There may be confusion/annoyance though as you will always be shown the contents of your .git directory as "new" files (unless you do update -P
- prune empty directories from working copy). Also anyone checking out the module from CVS will get the empty .git directories and may be confused by them.
If any of that sounds like a problem, the following question has some workarounds: