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Store::validate_pending_indexes cloned the entire node map on every apply() call even when no unique secondary index was defined, an O(store size) cost per write. Added the same early-return guard its sibling validate_pending_schema already had for the no-op case.
Store::apply_with_identity's idempotency check re-read and re-parsed the entire on-disk mutation log on every identity-bearing apply() — which Graph::transaction() always triggers, since it synthesizes a transaction id — turning transaction cost into O(total historical mutation count) per call. Replaced with an in-memory identity cache kept in sync with the durable log.