fix(cli-kit): respect package manager when installNodeModules adds specific packages

[andromia3]

WHY are these changes introduced?

Fixes #7042.

`installNodeModules()` in `packages/cli-kit/src/public/node/node-package-manager.ts` always ran ` install `, but `yarn`, `pnpm`, and `bun` all require the `add` subcommand to install a specific package with a version specifier — their `install` subcommand installs from the lockfile.

So a call like
```ts
installNodeModules({packageManager: 'yarn', args: ['@shopify/hydrogen@2025.7.1']})
```
produced `yarn install @shopify/hydrogen@2025.7.1`, which yarn rejects. Same for pnpm. Hydrogen PR #3462 worked around this by bypassing `installNodeModules()` with a direct `exec()` call that mapped the subcommand per package manager; this upstream fix lets that workaround be removed (@kdaviduik's original suggestion).

WHAT is this pull request doing?

Rather than silently change the meaning of `args` — which would break `packages/app/src/cli/services/init/template/npm.ts`, the only other call site, which uses `args` for flags like `['--network-concurrency', '1']` — added a new optional `packages?: string[]` field to `InstallNodeModulesOptions`.

When `packages` is provided:

• `npm` keeps using `install` (no change, and npm supports both).
• `yarn`, `pnpm`, and `bun` use `add`, matching the existing internal helpers `argumentsToAddDependenciesWith{Yarn,PNPM,Bun}` further down the same file.

When `packages` is omitted the function behaves identically to before, so every existing call site is unaffected.

```diff

• let args = ['install']

• const hasPackages = Boolean(options.packages?.length)
• const usesAddSubcommand =
• hasPackages &&
• (options.packageManager === 'yarn' ||

•  options.packageManager === 'pnpm' ||
  

•  options.packageManager === 'bun')
  

• let args = [usesAddSubcommand ? 'add' : 'install']
• if (options.packages) {
• args = args.concat(options.packages)
• }
  if (options.args) {
  args = args.concat(options.args)
  }
  ```

Full-path trace

• `installNodeModules` is used from two files inside this repo: `packages/app/src/cli/services/init/template/npm.ts` (passes `args` as flags, not packages) and `packages/app/src/cli/services/generate/extension.ts` (calls without `args` — pure lockfile install). Neither is affected by this change.
• External consumers (Hydrogen's `upgrade` command, among others) previously worked around the bug; they can migrate to the new `packages` field when they want to drop the workaround.
• The existing internal helpers `addNPMDependencies` / `argumentsToAddDependenciesWith{Yarn,PNPM,Bun}` already use `add` for yarn/pnpm/bun — this fix brings `installNodeModules` in line with the same convention when it's used to add specific packages.
• The `homebrew` and `unknown` `PackageManager` variants keep the existing `install` behaviour (`homebrew install ` isn't reachable in practice — `addNPMDependencies` throws for it — and `unknown` is an error state).

How to test your changes?

Six new tests in `packages/cli-kit/src/public/node/node-package-manager.test.ts`:

1. `uses `install` when packages are provided for npm`
2. `uses `add` when packages are provided for yarn`
3. `uses `add` when packages are provided for pnpm`
4. `uses `add` when packages are provided for bun`
5. `appends `args` after `packages`` — verifies ordering when both are passed
6. `uses `install` (unchanged) when no packages are provided, even for yarn` — regression guard for the existing `init/template/npm.ts` call path

Run locally:
```bash
pnpm --filter @shopify/cli-kit test node-package-manager
```

Post-release steps

None in this repo. Downstream note: Hydrogen's `upgrade.ts` workaround can be removed once this change ships in a `@shopify/cli-kit` release and a matching Hydrogen PR is opened.

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows) — no OS-specific code
• I've considered possible documentation changes — the new option has a JSDoc block explaining when to use it
• I've considered analytics changes to measure impact — N/A
• The change is user-facing, so I've added a changelog entry with `pnpm changeset add` — `.changeset/fix-install-node-modules-subcommand.md`, patch bump for `@shopify/cli-kit`