I think the externality of issue tracking systems like Jira (or even GitHub) cause friction. Literate programming has everything in one place.

I’d like to have a good issue tracking system inside git. I think the SQLite version management system has this functionality but I never used it.

One thing to solve is that different kinds of users need to interact with it in different kinds of ways. Non-programmers can use Jira, for example. Issues are often treated as mutable text boxes rather than versioned specification (and git is designed for the latter). It’s tricky!