Issues could live in /issues. Simple command-line (or GUI) tools could edit them. I'm thinking in particular of how password-store[0] makes tracking history in a git repo invisible: it Just Works™.
Discussions could live in /discussions, stored in something like RFC822 format. Again, simple CLI (or GUI, if you swing that way) tools could manipulate this easily.
A wiki can, again, live in the same repo.
PRs are a little different, since they really do need to live outside the repo. But what is a PR other than someone saying, 'hey, please pull my branch into yours'?
You have a `Product` repo and a `Product-meta` repo.
The biggest issue I have with using git as a truly decentralized system is remote management. Unless you want to be manually futzing with remotes on every single client and pushing/fetching from others correctly, you need some kind of central server.
I really think there is a hole here for a product that works with git underneath, but gives a nice easy way to manage all that complexity.
Unfortunately, no non-cli frontend exists right now (feel free to build one, shouldn't be complicated). Also some convenience is still missing, but could easily be integrated.
What's also missing is a way to give users of the tool access to a repository where they can submit issues (which then could also be used by a web/gui frontend for the tool). This is not the domain of git-dit itself, but a solution needs to be found. One idea would be a publish repo (where everyone can push) which automatically does some sanity-verification on the issues and forwards them to the maintainers repository... or something like that.
Also, https://github.com/vitiral/artifact/ is a really nice tool to do planning of an application or library inside a git repository. I am currently starting using it in iamg (https://imag-pim.org) and it is really wonderful. The author currently does a reimplementation of its core functionality to make it even more powerful.
Every now and then I sketch ideas on the subject, but haven't yet gotten someone to pay me to build it. ;)