[Bug] Error building express remix after updating hydrogen to version 2025.1.3

[arditdine]

What is the location of your example repository?

No response

Which package or tool is having this issue?

Hydrogen

What version of that package or tool are you using?

latest

What version of Remix are you using?

2.16.4

Steps to Reproduce

Start a new project using the express template npm create @shopify/hydrogen@latest -- --template express
set NODE_ENV to development or just update package.json

"scripts": {
    "build": "cross-env NODE_ENV=development remix vite:build",
    ...
}

run npm run build and the build will fail

Expected Behavior

To successfully build with NODE_ENV=development

Actual Behavior

After the new update for March release that included vite 6, remix 2.16 and hydrogen 2025.1.3
When I build the production application using remix vite:build it's working fine

But when i try to build the application using NODE_ENV=developement remix vite:build
I get the following warning

transforming (22) node_modules\@shopify\hydrogen\dist\vite\virtual-routes\routes\index.jsx
new URL("../", import.meta.url) doesn't exist at build time, it will remain unchanged to be resolved at runtime. If this is intended, you can use the /* @vite-ignore */ comment to suppress this warning.

It start building a bunch of components and routes and then it fails with the following error

[remix-virtual-modules] Could not load virtual:remix/server-manifest (imported by virtual:remix/server-build): No manifest entry found for "app/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/layout.jsx". Known manifest keys: "C:/Users/al/dev/hydrogen-express/app/styles/app.css", "C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/debug-network.css", "C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/styles.css", "_components-DnH0wNCc.js", "_favicon-CG_43MKL.js", "_index-Cax_LsAE.js", "_scroll-restoration-D-fGmlvo.js", "app/entry.client.tsx", "app/root.tsx?__remix-build-client-route", "app/routes/_index.tsx?__remix-build-client-route", "app/routes/products.$handle.tsx?__remix-build-client-route", "node_modules/@shopify/hydrogen/dist/development/log-seo-tags-IG37ONQ2.js", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/favicon-dark.svg", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/favicon.svg", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/inter-variable-font.woff2", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/jetbrainsmono-variable-font.woff2", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/layout.jsx?__remix-build-client-route", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/graphiql.jsx?__remix-build-client-route", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/index.jsx?__remix-build-client-route", "node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/subrequest-profiler.jsx?__remix-build-client-route"
    at resolveChunk (C:\Users\al\dev\hydrogen-express\node_modules\@remix-run\dev\dist\vite\plugin.js:156:11)
    at getRemixManifestBuildAssets (C:\Users\al\dev\hydrogen-express\node_modules\@remix-run\dev\dist\vite\plugin.js:161:20)
    at generateRemixManifestsForBuild (C:\Users\al\dev\hydrogen-express\node_modules\@remix-run\dev\dist\vite\plugin.js:519:12)
    at processTicksAndRejections (node:internal/process/task_queues:95:5)
    at Object.getRemixServerManifest (C:\Users\al\dev\hydrogen-express\node_modules\@remix-run\dev\dist\vite\plugin.js:420:44)
    at Object.load (C:\Users\al\dev\hydrogen-express\node_modules\@remix-run\dev\dist\vite\plugin.js:932:50)
    at PluginDriver.hookFirstAndGetPlugin (file:///C:/Users/al/dev/hydrogen-express/node_modules/rollup/dist/es/shared/node-entry.js:22038:28)
    at file:///C:/Users/al/dev/hydrogen-express/node_modules/rollup/dist/es/shared/node-entry.js:21036:33
    at Queue.work (file:///C:/Users/al/dev/hydrogen-express/node_modules/rollup/dist/es/shared/node-entry.js:22266:32) {
  code: 'PLUGIN_ERROR',
  plugin: 'remix-virtual-modules',
  hook: 'load',
  watchFiles: [
    'C:/Users/al/dev/hydrogen-express/app/entry.server.tsx',
    'C:/Users/al/dev/hydrogen-express/app/root.tsx',
    'C:/Users/al/dev/hydrogen-express/app/routes/products.$handle.tsx',
    'C:/Users/al/dev/hydrogen-express/app/routes/_index.tsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/layout.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/graphiql.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/subrequest-profiler.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/routes/index.jsx',
    'C:\\Users\\al\\dev\\hydrogen-express\\package.json',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/Layout.jsx',
    'node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/favicon.svg',
    'node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/favicon-dark.svg',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/RequestWaterfall.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/lib/useDebugNetworkServer.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/RequestTable.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconDiscard.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconClose.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/RequestDetails.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/styles.css',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/HydrogenLogoBaseBW.jsx',
    'node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/jetbrainsmono-variable-font.woff2',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/HydrogenLogoBaseColor.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconGithub.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconTwitter.jsx',
    'node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/inter-variable-font.woff2',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconBanner.jsx',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/assets/debug-network.css',
    'C:/Users/al/dev/hydrogen-express/node_modules/@shopify/hydrogen/dist/vite/virtual-routes/components/IconError.jsx'
  ]
}