fix: use direct serialization instead of clone in _serializeItems

Per review feedback from @AustinMroz: replace clone().serialize() with
direct serialization for all nodes, clearing links manually. Avoids the
clone->serialize gap where transient nodes lose external state.

src/lib/litegraph/src/LGraphCanvas.ts

@@ -3902,25 +3902,21 @@ export class LGraphCanvas implements CustomEventDispatcher<LGraphCanvasEventMap>
         // Nodes
         if (item.clonable === false) continue
 
-        // SubgraphNodes must serialize the original instance directly,
-        // because clone() creates a transient node whose serialize() queries
-        // promotionStore with the wrong id → stale proxyWidgets. (#9976)
-        const cloned =
-          item instanceof SubgraphNode
-            ? LiteGraph.cloneObject(item.serialize())
-            : item.clone()?.serialize()
+        // Serialize the original node directly instead of clone().serialize().
+        // clone() creates a transient node whose state can diverge from the
+        // original (e.g. SubgraphNode promotionStore keyed by wrong id,
+        // PrimitiveNode losing widgets_values). ID deduplication is already
+        // handled on the deserialize side by _deserializeItems. (#9976)
+        const cloned = LiteGraph.cloneObject(item.serialize())
         if (!cloned) continue
 
-        // Clear links on the serialized copy (clone() does this internally;
-        // for the direct-serialize path we must do it explicitly).
-        if (item instanceof SubgraphNode) {
-          if (cloned.inputs) {
-            for (const input of cloned.inputs) input.link = null
-          }
-          if (cloned.outputs) {
-            for (const output of cloned.outputs) {
-              if (output.links) output.links.length = 0
-            }
+        // Clear links on the serialized copy (clone() used to do this).
+        if (cloned.inputs) {
+          for (const input of cloned.inputs) input.link = null
+        }
+        if (cloned.outputs) {
+          for (const output of cloned.outputs) {
+            if (output.links) output.links.length = 0
           }
         }
 

src/lib/litegraph/src/subgraph/SubgraphNode.serialize.test.ts

@@ -3,9 +3,9 @@
  *
  * Verifies:
  * 1. serialize() correctly captures instance-scoped promotion metadata
- * 2. The _serializeItems copy path should not use clone() for SubgraphNodes
- *    (clone creates a transient node with wrong id, whose serialize() queries
- *     promotionStore with the wrong key → empty/stale proxyWidgets)
+ * 2. Direct serialization (without clone()) preserves correct state — the
+ *    _serializeItems path uses item.serialize() for all nodes, avoiding the
+ *    clone→serialize gap where transient nodes lose external state
  * 3. Subgraph definition serialization preserves modified widget values
  *
  * @see https://github.com/Comfy-Org/ComfyUI_frontend/issues/9976
@@ -181,14 +181,12 @@ describe('SubgraphNode.serialize() state isolation (#9976)', () => {
     expect(serializedNode?.widgets_values?.[0]).toBe(777)
   })
 
-  it('_serializeItems should not use clone().serialize() for SubgraphNodes', () => {
+  it('direct serialize() preserves proxyWidgets and widget values', () => {
     const { subgraph, interiorNode, subgraphNode } =
       createSubgraphWithWidgetNode()
 
-    // The correct approach: serialize the ORIGINAL node directly
+    // Direct serialization captures correct proxyWidgets
     const originalSerialized = subgraphNode.serialize()
-
-    // proxyWidgets should reflect the original node's promotions
     expect(originalSerialized.properties?.proxyWidgets).toEqual([
       [String(interiorNode.id), 'seed']
     ])

src/lib/litegraph/src/subgraph/SubgraphNode.ts

@@ -926,6 +926,10 @@ export class SubgraphNode extends LGraphNode implements BaseLGraph {
   override _internalConfigureAfterSlots() {
     this._rebindInputSubgraphSlots()
 
+    // Prune inputs that don't map to any subgraph slot definition.
+    // This prevents stale/duplicate serialized inputs from persisting (#9977).
+    this.inputs = this.inputs.filter((input) => input._subgraphSlot)
+
     // Ensure proxyWidgets is initialized so it serializes
     this.properties.proxyWidgets ??= []
 
@@ -1439,9 +1443,13 @@ export class SubgraphNode extends LGraphNode implements BaseLGraph {
     return super.serialize()
   }
   override clone() {
-    // Note: _serializeItems bypasses clone() for SubgraphNodes to avoid
-    // promotionStore identity mismatch (#9976). This clone path is still
-    // used by alt+drag and other operations.
-    return super.clone()
+    const clone = super.clone()
+
+    //TODO: Consider deep cloning subgraphs here.
+    //It's the safest place to prevent creation of linked subgraphs
+    //But the frequency of clone().serialize() calls is likely to result in
+    //pollution of rootGraph.subgraphs
+
+    return clone
   }
 }