update method
Updates a node in the spatial index.
Call this after any change to node position or size. Also updates all port positions for this node.
Implementation
void update(Node<T> node) {
_nodes[node.id] = node;
final item = NodeSpatialItem(nodeId: node.id, bounds: node.getBounds());
_grid.addOrUpdate(item);
// Update port positions for this node
_updatePortsForNode(node);
_autoFlush();
_notifyChanged();
}