fix: prune orphaned SubgraphNode inputs after configure (#10020)

## Summary

Prune orphaned inputs in `_internalConfigureAfterSlots()` to fix
duplicate SubgraphNode inputs that accumulate on serialize-load cycles.

## Changes

- **What**: After `_rebindInputSubgraphSlots()`, filter out inputs with
no matching `_subgraphSlot`. This prevents `LGraphNode.configure()`
`cloneObject` expansion from persisting stale duplicates.
- Added 3 regression tests covering: corrupted serialized data,
reconfigure round-trips, and serialization output.

## Review Focus

The fix is a single `filter()` call. The existing `console.warn` guard
at line ~976 (for inputs without `_subgraphSlot`) becomes dead code
after this fix but is retained as defense-in-depth.

Fixes #9977

┆Issue is synchronized with this [Notion
page](https://www.notion.so/PR-10020-fix-prune-orphaned-SubgraphNode-inputs-after-configure-3256d73d3650812e8cecf4a3c86f2c33)
by [Unito](https://www.unito.io)

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

@@ -9,9 +9,9 @@ import { describe, expect, it, vi } from 'vitest'
 import { createTestingPinia } from '@pinia/testing'
 import { setActivePinia } from 'pinia'
 
-import type { SubgraphNode } from '@/lib/litegraph/src/litegraph'
-import { LGraph, Subgraph } from '@/lib/litegraph/src/litegraph'
+import { LGraph, Subgraph, SubgraphNode } from '@/lib/litegraph/src/litegraph'
 import type { SubgraphInput } from '@/lib/litegraph/src/subgraph/SubgraphInput'
+import type { ExportedSubgraphInstance } from '@/lib/litegraph/src/types/serialisation'
 
 import { subgraphTest } from './__fixtures__/subgraphFixtures'
 import {
@@ -618,6 +618,86 @@ describe.skip('SubgraphNode Cleanup', () => {
   })
 })
 
+describe('SubgraphNode duplicate input pruning (#9977)', () => {
+  it('should prune inputs that have no matching subgraph slot after configure', () => {
+    setActivePinia(createTestingPinia({ stubActions: false }))
+
+    const subgraph = createTestSubgraph({
+      inputs: [
+        { name: 'a', type: 'STRING' },
+        { name: 'b', type: 'NUMBER' }
+      ]
+    })
+
+    const parentGraph = new LGraph()
+    const instanceData = {
+      id: 1 as const,
+      type: subgraph.id,
+      pos: [0, 0] as [number, number],
+      size: [200, 100] as [number, number],
+      inputs: [
+        { name: 'a', type: 'STRING', link: null },
+        { name: 'b', type: 'NUMBER', link: null },
+        { name: 'a', type: 'STRING', link: null },
+        { name: 'b', type: 'NUMBER', link: null }
+      ],
+      outputs: [],
+      properties: {},
+      flags: {},
+      mode: 0,
+      order: 0
+    }
+
+    const node = new SubgraphNode(
+      parentGraph,
+      subgraph,
+      instanceData as ExportedSubgraphInstance
+    )
+
+    expect(node.inputs).toHaveLength(2)
+    expect(node.inputs.every((i) => i._subgraphSlot)).toBe(true)
+  })
+
+  it('should not accumulate duplicate inputs on reconfigure', () => {
+    setActivePinia(createTestingPinia({ stubActions: false }))
+
+    const subgraph = createTestSubgraph({
+      inputs: [
+        { name: 'a', type: 'STRING' },
+        { name: 'b', type: 'NUMBER' }
+      ]
+    })
+
+    const node = createTestSubgraphNode(subgraph)
+    expect(node.inputs).toHaveLength(2)
+
+    const serialized = node.serialize()
+    node.configure(serialized)
+    expect(node.inputs).toHaveLength(2)
+
+    const serialized2 = node.serialize()
+    node.configure(serialized2)
+    expect(node.inputs).toHaveLength(2)
+  })
+
+  it('should serialize with exactly the subgraph-defined inputs', () => {
+    setActivePinia(createTestingPinia({ stubActions: false }))
+
+    const subgraph = createTestSubgraph({
+      inputs: [
+        { name: 'x', type: 'IMAGE' },
+        { name: 'y', type: 'VAE' }
+      ]
+    })
+
+    const node = createTestSubgraphNode(subgraph)
+    const serialized = node.serialize()
+
+    expect(serialized.inputs).toHaveLength(2)
+    expect(serialized.inputs?.map((i) => i.name)).toEqual(['x', 'y'])
+  })
+})
+
 describe('SubgraphNode promotion view keys', () => {
   it('distinguishes tuples that differ only by colon placement', () => {
     setActivePinia(createTestingPinia({ stubActions: false }))

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 ??= []