`leafCursorStale` was only cleared inside `captureTurnTreeRefs`, but
`registerThread` and `rollbackThread` also re-baseline `lastKnownLeaf` from
a full `get_entries`. After one failed capture the flag therefore stuck, so
later turns kept skipping their `nativeTurnRef` and rollback across them
failed with no captured session-tree entry.

Both re-baseline sites now clear the flag, and only leave it set when the
listing itself failed. An empty tree is a success with no leafId.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>