Don't avoid drawing lines over groups that we're coming to or from.

Layout.js

@@ -3,6 +3,7 @@ class Layout {
     this.graph_ = graph;
 
     this.nodes_ = [];
+    // TODO: value should be a set, not a single value, for groups
     this.nodesByPos_ = new StringMap();
     this.nodesByGraphNode_ = new Map();
     this.linksByPos_ = new StringMap();

LayoutGroup.js

@@ -6,7 +6,7 @@ class LayoutGroup {
     this.tension = 0;
 
     for (let node of nodes) {
-      node.groups.push(this);
+      node.groups.add(this);
     }
   }
 

LayoutLink.js

@@ -117,7 +117,13 @@ class LayoutLink {
     // arguments. That means that any costs applied to nodes must be applied
     // whether the node is from or to. Traversal is double-charged.
     for (let pos of [from, to]) {
-      if (this.nodesByPos_.has(pos)) {
+      let taken = this.nodesByPos_.get(pos);
+      if (taken instanceof LayoutGroup &&
+          (this.from_.groups.has(taken) ||
+           this.to_.groups.has(taken))) {
+        // We're going to or from this group, so traversing it is fine.
+        continue;
+      } else if (taken) {
         // Traversing nodes has higher cost
         cost += 5;
       };

LayoutNode.js

@@ -3,7 +3,7 @@ class LayoutNode {
     this.graphNode_ = graphNode;
     this.nodesByPos_ = nodesByPos;
     this.pos = pos;
-    this.groups = [];
+    this.groups = new Set();
 
     this.nodesByPos_.set(this.pos, this);
   }