Fix sublayers not persisted on save

- SaveStage: explicitly call rootLayer->Save() before m_stage->Save() to
  ensure root-layer metadata (subLayers field) is always written to disk
- SaveUsdFile: redirect to SaveAs when the root layer is anonymous so
  Ctrl+S on an in-memory stage no longer silently does nothing
- SaveUsdFileAs: call RefreshManagers() after SaveStageAs so LayerManager
  stays in sync with the newly opened file-backed stage; without this,
  sublayers added after a Save As went to the old stale stage and were lost
- LayerCreateCommand::Execute: use GetSublayers() (sublayer-local indices)
  instead of GetLayerStack() (full-stack indices) to record m_insertedIndex,
  fixing undo of add-sublayer removing the wrong layer

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

src/ui/Application.cpp

@@ -397,7 +397,15 @@ void Application::SaveUsdFile() {
     if (!m_stageManager->HasStage()) {
         return;
     }
-    
+
+    // If the current stage is in-memory (anonymous root layer), fall through to
+    // Save As — UsdStage::Save() cannot write anonymous layers to disk.
+    auto rootLayer = m_stageManager->GetRootLayer();
+    if (!rootLayer || rootLayer->IsAnonymous()) {
+        SaveUsdFileAs();
+        return;
+    }
+
     if (!m_stageManager->SaveStage()) {
         LOG_ERROR("Failed to save USD file: " + m_stageManager->GetLastError());
     }
@@ -407,17 +415,23 @@ void Application::SaveUsdFileAs() {
     if (!m_stageManager->HasStage()) {
         return;
     }
-    
+
     std::string filePath = FileDialog::SaveFile(
         "USD Files (*.usd;*.usda;*.usdc)\0*.usd;*.usda;*.usdc\0All Files (*.*)\0*.*\0",
         "Save USD File As",
         "usd",
         m_imguiContext->GetWindowHandle()
     );
-    
+
     if (!filePath.empty()) {
         if (!m_stageManager->SaveStageAs(filePath)) {
             LOG_ERROR("Failed to save USD file: " + m_stageManager->GetLastError());
+        } else {
+            // SaveStageAs reopens m_stageManager's stage from the new file path.
+            // RefreshManagers syncs m_layerManager (and others) to that new stage;
+            // without this, subsequent sublayer edits go to the old (now stale) stage
+            // and are silently lost on the next save.
+            RefreshManagers();
         }
     }
 }