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/state/src/extract.rs

@@ -29,6 +29,17 @@ pub fn apply_rollout_item(
     }
 }
 
+/// Return whether this rollout item can mutate thread metadata stored in SQLite.
+pub fn rollout_item_affects_thread_metadata(item: &RolloutItem) -> bool {
+    match item {
+        RolloutItem::SessionMeta(_) | RolloutItem::TurnContext(_) => true,
+        RolloutItem::EventMsg(EventMsg::TokenCount(_) | EventMsg::UserMessage(_)) => true,
+        RolloutItem::EventMsg(_) | RolloutItem::ResponseItem(_) | RolloutItem::Compacted(_) => {
+            false
+        }
+    }
+}
+
 fn apply_session_meta_from_item(metadata: &mut ThreadMetadata, meta_line: &SessionMetaLine) {
     if metadata.id != meta_line.meta.id {
         // Ignore session_meta lines that don't match the canonical thread ID,