This is a super interesting space, and lots of fun and difficult problems to tackle.
A few trailheads of interesting complexity:
1. Concurrent machine edits - in particular handling links to renamed files across devices. This is a case where CRDTs fall over because they converge but are not idempotent. For example renaming a file [[hello 1]] to [[hello 2]] when multiple devices are online can result in [[hello 22]] because deletes merge before inserts.
2. Ingesting disk edits in the age of claude code. The intended behavior can change based on what I'm calling the "intent fidelity spectrum". I've been using that spectrum as a guide for when to apply merges in "text space" vs. "crdt space", including sometimes withholding ops based on origin (e.g. from obsidian processFile calls), cancelling them) or offline status. For example, if you made edits while offline and have a least-common-ancestor you may be able to look for conflicts via diff3 and then conditionally use diff-match-patch if there are no conflicts, or surface the conflict to the user if there's not a good merge strategy based on the low levels of intent.
3. History and memory management - how do you recover state if a user has a competing sync service which causes an infinite loop in file creation/deletion. This can be difficult with CRDTs because the tombstones just keep syncing back and forth between peers and can be difficult to clear. This is significantly worse if you use Y.PermanentUserData (do not recommend...).