fixed z-index ordering issues

packages/system/src/styles/init.css

@@ -123,6 +123,11 @@
   }
 }
 
+.xy-flow__edge-wrapper {
+  position: absolute;
+  overflow: visible;
+}
+
 .xy-flow__edge {
   pointer-events: visibleStroke;
 
@@ -144,10 +149,6 @@
     pointer-events: none;
   }
 
-  &:focus {
-    outline: 1px solid red !important;
-  }
-
   &.selected,
   &:focus,
   &:focus-visible {
@@ -437,3 +438,7 @@ svg.xy-flow__connectionline {
     }
   }
 }
+
+.xy-flow__marker {
+  position: absolute;
+}

packages/system/src/utils/store.ts

@@ -196,8 +196,9 @@ function updateChildNode<NodeType extends NodeBase>(
   }
 }
 
+const DEFAULT_NODE_Z = 1;
 function calculateZ(node: NodeBase, selectedNodeZ: number) {
-  return (isNumeric(node.zIndex) ? node.zIndex : 0) + (node.selected ? selectedNodeZ : 0);
+  return (isNumeric(node.zIndex) ? node.zIndex : DEFAULT_NODE_Z) + (node.selected ? selectedNodeZ : DEFAULT_NODE_Z);
 }
 
 function calculateChildXYZ<NodeType extends NodeBase>(