There are several attempts at tracking issues inside a repository. What we really need to sell the concept, though, I think is one that can reasonably sync with GitHub Issues. GitHub Issues are a reasonable front end for issue reporting for casual and non-technical users and if you can interoperate with them you don't have to reinvent that basic CMS.

Every now and then I sketch ideas on the subject, but haven't yet gotten someone to pay me to build it. ;)