Do you specifically need GNU RCS? That's not seeing all that much development activity based on what's visible around the network; according to the Perdue RCS repository, 5.7 is current -- and RCS 5.6 was the version on Freeware V4.0 from a very long time ago.
If I needed RCS specifically, I might well look at the old port and re-port 5.7 over.
With CMS and multiple modules with the same or similar paths, that's usually done with either multiple CMS libraries, or by wrapping CMS and hacking up the names, or by using classes and shutting off the reference areas entirely.
(I've usually ended up shutting off the reference library stuff, as that has tended to lead to pain and skews; it works pretty well for simple environments, but not so well in the more complex. It's also possible to use CMS ACLs to simulate class-specific reference errors, but it's often just as easy and more maintainable to fetch what you need when you need it.)
The package used by OpenVMS Engineering to work within and occasionally work around some of the limits with CMS was VDE; that's on the Freeware. (That's probably not the best choice, but it can give you some ideas of what's possible with CMS and with the CMS APIs.)
Here, I'd probably look toward a (newer) package such as Mercurial (Hg); there is a Mercurial port around and that's rather newer than RCS and such. I'd check around, as there may be a git port available by now, too. Maybe Subversion (SVN) in a real pinch. But rcs and sccs are really, really old...
