Interesting, thanks for sharing!
I plan to give it my own shot with vibing my own harness; I plan to use https://glean.software/ as the central database for everything code, then for documentation. After that, it could be used for bookkeeping for reasoning in a style similar to what you describe; after all, Angle, the query language of Glean, is a https://en.wikipedia.org/wiki/Datalog with some extras (I don't know which yet), so stuff like onthologies could be queried quite well, I would guess.