The main hole is that ATProto's data model is a bit awkward for a code forge.
Issues/PRs/comments are records owned by their authors, not by the repo. So an issue can span N users' PDSes. That's a neat model for social media, but a forge wants the repo to be the durable owner/context of its issues and history because that's where the comment/issue/etc. logically belongs.
The solution? tangled.org acts as a super advanced cache/aggregator for that. What can possibly go wrong?
There's a good chance this will change in the future and the repo on the knot will also contain the social aspects of repos (issues, PRs, etc.)
> As time goes on we are re-assessing the idea of users owning what is "collaborative data" (issues, PRs, etc.) on their PDSes - soon may come the day that an issue also lives on the knot as a source of truth, with an accompanying pointer record on user PDS to attest that it's theirs.