Good programming calls for good organization -- including naming of files and directories. But the popular source-code management tool, CVS, makes that difficult.
I don't think anyone who's used CVS on a new project is unaware of these problems. Predictably the first comment is, If that's so objectionable, why don't you fix it?
but really, why hasn't someone fixed it yet? The author points out it'd be non-trivial (his word) to fix, since all CVS data is keyed to filename. (The author also doesn't have a personal web page or any project listings, but is ranked Journeyer so must know something. Like I said, I agree with the idea of the article.)
The reason no one's fixed it yet is given in the other comments (of the three there currently): rather than fixing this flaw so fundamental to CVS, they write their own versioning systems from scratch. I don't know for sure, but it sounds like one would have to do that anyway to fix the flaw. The best one might hope for is a completely new system with as similar a UI as possible.
(Meanwhile, considered harmful is still considered harmful. Friends don't let friends write Foo Considered Harmful.)