fix: upgrade xrefs

packages/myst-cli/src/transforms/crossReferences.ts

@@ -1,5 +1,6 @@
 import type { VFile } from 'vfile';
 import { selectAll } from 'unist-util-select';
+import { visit } from 'unist-util-visit';
 import type { FrontmatterParts, GenericNode, GenericParent, References } from 'myst-common';
 import { RuleId, fileWarn, plural, selectMdastNodes } from 'myst-common';
 import { computeHash, tic } from 'myst-cli-utils';
@@ -32,6 +33,24 @@ export type MystData = {
   references?: References;
 };
 
+function upgradeMystData(data: MystData): MystData {
+  // Visit outputs
+  visit(
+    data.mdast as any,
+    'output',
+    (node: GenericNode, index: number | null, parent: GenericParent | null) => {
+      if (parent && parent.type !== 'outputs') {
+        const outputs = {
+          type: 'outputs',
+          children: [node],
+        };
+        parent.children[index!] = outputs;
+      }
+    },
+  );
+  return data;
+}
+
 async function fetchMystData(
   session: ISession,
   dataUrl: string | undefined,
@@ -48,7 +67,8 @@ async function fetchMystData(
     try {
       const resp = await session.fetch(dataUrl);
       if (resp.ok) {
-        const data = (await resp.json()) as MystData;
+        const data = upgradeMystData((await resp.json()) as MystData);
+
         writeToCache(session, filename, JSON.stringify(data));
         return data;
       }