feat(ci): add scaffolding tests for npm, pnpm, and yarn

[itsjustriley]

WHY are these changes introduced?

Resolves developer-tools-team/issues/1042

There were no CI checks validating that create-hydrogen correctly scaffolds projects with different package managers. A bug in handleDependencies was silently causing --package-manager to be ignored when --install-deps was explicitly true — all scaffolded projects used npm regardless of the specified package manager.

WHAT is this pull request doing?

CI scaffolding tests — Adds a new test_scaffolding job to CI that uses a GitHub Actions matrix to test each package manager (npm, pnpm, yarn, bun) in parallel. Each matrix entry:

1. Installs the package manager (if not pre-installed)
2. Runs create-hydrogen with --package-manager
3. Verifies the correct lockfile exists
4. Builds the scaffolded app

Bug fix — Adds a missing else branch in handleDependencies
(packages/cli/src/lib/onboarding/common.ts). When --install-deps was true and --package-manager was a known PM (not unknown), actualPackageManager stayed as the default 'npm' because neither the unknown nor undefined branches executed.

Unit test — Verifies that setupTemplate with installDeps: true and packageManager: 'pnpm' calls installNodeModules with pnpm.

HOW to test your changes?

The CI scaffolding tests run automatically on the PR.

Checklist

• I've read the https://github.com/Shopify/hydrogen/blob/main/CONTRIBUTING.md
• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've added a https://github.com/Shopify/hydrogen/blob/main/CONTRIBUTING.md#changesets if this
  PR contains user-facing or noteworthy changes
• I've added https://github.com/Shopify/hydrogen/blob/main/CONTRIBUTING.md#testing to cover my
  changes

[shopify]

Oxygen deployed a preview of your add-e2e-tests-for-package-managers branch. Details:

Storefront	Status	Preview link	Deployment details	Last update (UTC)
Skeleton (skeleton.hydrogen.shop)	⏳ In progress (Logs)	-	Inspect deployment	February 10, 2026 2:58 PM

Learn more about Hydrogen's GitHub integration.

[fredericoo]

code looks great but tests with bun will fail until this or this lands