I don't know if this really solves anything, but GitHub does have support for commenting on commits. So linking to a new Arc Forum post from an old Anarki commit is already as trivial as linking the other way around. The problem is that nobody's looking there (right?).
How about having every Anarki commit be a forum topic after all, but having those topics be hidden on a separate "commit log" page until someone promotes them?
Independent of the webapp I'd like to suggest the best practice of inserting a permalink to a relevant repo at least once during a thread.
Often when I dive into the AF archives I find people talking about variants of arc semantics that it's a lot of trouble to reconstruct. I'm guilty of this as well with wart and whatnot. At the time the context was clear to the participants, but they've since moved on. We could find the context in some nearby thread, but it's hard to locate nearby threads. The only thing that's easy is clicking parent again and again until we get to the top, then doing a search for a github link or something.