I see in the post that lexicon has been finalized. Does that include putting the issue, pr & comment records under the repo scope instead of the user scope?

I am asking because I have been waiting for that change. I intend to make all the public repos from https://juju.bi (code forge I am building) interoperable with Tangled and basically behave as knot server.

Indeed. Repos own issues and pulls now! We will publish a post on how we do this very soon (hint: we store them as git objects within the repository and project them as an AT Protocol MST -- hence making knots PDS-like).