https://github.com/neithernut/git-dit provides a distributed issue tracker inside git, without cluttering the repository with unneeded files and also gives the possibility for having tree-like conversation, referencing issues and so on.

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.