fix merge script sqlite locking

scripts/merge_cluster_embeddings.py

@@ -195,12 +195,16 @@ def main() -> None:
 
     with store._conn() as conn:  # noqa: SLF001
         for topic, bucket in groups:
-            rep = bucket[0]
-            rep_id = rep.get("cluster_id")
             merged = _merge_payloads(bucket)
-            store.upsert_clusters([merged], topic=topic)
+            cluster_id = merged.get("cluster_id")
+            payload = json.dumps(merged, ensure_ascii=False)
+            conn.execute(
+                "INSERT INTO clusters(cluster_id, topic, payload, updated_at) VALUES(?,?,?,?) "
+                "ON CONFLICT(cluster_id) DO UPDATE SET topic=excluded.topic, payload=excluded.payload, updated_at=excluded.updated_at",
+                (cluster_id, topic, payload, merged.get("last_updated") or merged.get("updated_at") or ""),
+            )
             # Delete absorbed duplicates; keep the representative row.
-            dup_ids = [c.get("cluster_id") for c in bucket[1:] if c.get("cluster_id")]
+            dup_ids = [c.get("cluster_id") for c in bucket if c.get("cluster_id") != cluster_id]
             for cid in dup_ids:
                 conn.execute("DELETE FROM clusters WHERE cluster_id=?", (cid,))
         conn.commit()