It's not a silly CVS question - it's a question about silly CVS!
There are only 2 ways I know that you can add a directory to a project and get it into CVS without explicitly telling CVS to add it: The Eclipse
IDE and the Emacs
Java plugin. These 2 IDE systems are smart enough to figure that if you added a directory to a source-code-managed project and you didn't explicitly exclude it from source code management, that by gosh, maybe you actually
wanted it to be source-code managed.
The stock CVS tools, both command-line and GUI (e.g. Tortoise), and even the IntelliJ IDE have to be
explicitly told to add the directory to CVS, or it won't go in, and someday years later when you check out a clean copy for an emergency build, you'll find that out the hard way. Although if you manage things using the right IDE options in Intellij, it might have given you a small
boost.
If I sound bitter, it's because I've learned such things at my cost.
There's another complication, as well. CVS doesn't ever actually archive
directories, only
files. So even the "helpful" IDEs won't add empty directories - at least one file has to be present in that directory before it will get added to the archive, even if it's just a dummy file.
Subversion was developed more or less specifically because of this problem and the related problem that CVS isn't very good at tracking file and directory rename operations. Subversion has its own annoyances, however. I'll leave them for another time.