Remove some deprecated subdependencies

Author: gonzaloriestra

package.json

@@ -42,7 +42,7 @@
     "@changesets/cli": "2.29.7",
     "@graphql-codegen/add": "6.0.0",
     "@graphql-codegen/cli": "6.0.1",
-    "@graphql-codegen/near-operation-file-preset": "3.1.0",
+    "@graphql-codegen/near-operation-file-preset": "4.0.0",
     "@graphql-codegen/typed-document-node": "6.1.0",
     "@graphql-codegen/typescript-operations": "5.0.2",
     "@nx/eslint-plugin": "22.0.2",

packages/ui-extensions-dev-console/package.json

@@ -29,7 +29,7 @@
     "@types/react": "^18.2.0",
     "@types/react-dom": "^18.2.0",
     "@vitejs/plugin-react": "^5.1.4",
-    "jsdom": "^20.0.3",
+    "jsdom": "^25.0.0",
     "sass": "^1.83.1",
     "vite": "6.4.1"
   }

packages/ui-extensions-server-kit/package.json

@@ -56,7 +56,7 @@
     "@shopify/ui-extensions-test-utils": "3.26.0",
     "@types/react": "^18.2.0",
     "@vitejs/plugin-react": "^5.1.4",
-    "jsdom": "^20.0.3",
+    "jsdom": "^25.0.0",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "vite": "6.4.1"