I know these problems far too well, so I'm totally with you when you talk about time constraints :). I struggle with some of my projects a lot too.
Renaming branches in git is pretty straightforward. Basically what you need to do is rename the branch locally, delete the remote branch and push the renamed branch. But you have to be careful, you need to have the branch you'd like to rename checked out (at least it has happened to me in the past, that things got messed up when I was renaming a branch that wasn't currently checked out.). The sequence would be as follows:
# git checkout master
# git branch -m master ipv6
# git push origin :master
# git push origin ipv6
# git checkout ipv4
# git branch -m ipv4 master
# git push origin :ipv4
# git push origin master
This should basically "exchange" the branches. Also I think it should not mess with other peoples forks/clones, at least I read that all should be fine :). The important things are the colons in front of the branchname in the first push (git push origin :master) and the third push (git push origin :ipv4) as this basically translates to "delete that branch in the remote" (a more precise explanation can be found here:
http://stackoverflow.com/questions/9524933/renaming-a-branch-in-github). If you are running git 1.7 or later you could alternatively do "git push origin --delete master" and "git push origin --delete ipv4" respectively. If you like, I will try this out on my fork, before we mess up the original repo ;).
Regarding cmake, as I said i prefer it because in my opinion, its much easier to handle when crossing platform border as we do. I am currently working on the cmake stuff and hope to have it ready by sunday evening.
Lastly I would be happy to help out on the IPv6 stuff as it would be a great opportunity to delve deeper in to this matter which would be good for my studies in computer science :).
To sum it up, I'll try the branch-magic when I'm finished with the cmake transition and afterwards start working on the IPv6 implementation.
Regards,
Felix