chore: improve DB flushing (#13620)

This branch:
* Avoid flushing DB when not necessary
* Filter events for which we perfom an `upsert` into the DB
* Add a dedicated update function of the `thread:updated_at` that is
lighter

This should significantly reduce the DB lock contention. If it is not
sufficient, we can de-sync the flush of the DB for `updated_at`

codex-rs/core/src/codex.rs

@@ -1694,7 +1694,7 @@ impl Session {
         self.services.state_db.clone()
     }
 
-    /// Ensure all rollout writes are durably flushed.
+    /// Ensure rollout file writes are durably flushed.
     pub(crate) async fn flush_rollout(&self) {
         let recorder = {
             let guard = self.services.rollout.lock().await;