The latter is typically the realm of requirements, design documentation, and possibly test plans.
Generating such documentation from code seems quite impossible, or at least wrong.
It is unfortunate that most open source software is lacking in such documentation, giving off bad signals to junior developers.
Edit: not to take away from the product being discussed here, which seems very useful! I am merely supporting the parent here.
You forgot one of the biggest spots for "why" documentation... git commit messages, where the point is to say why you made this change. Maybe taking into account the commit messages around the code in question would help.
Still a great idea, though. Ingesting all data from JIRA may be beneficial as well.