[Tests] Remove filesystem mocks in app init command tests

[gonzaloriestra]

WHY are these changes introduced?

Filesystem mocking can lead to tests that don't accurately reflect real-world behavior and are brittle to changes in the underlying implementation of filesystem utilities.

WHAT is this pull request doing?

Refactors packages/app/src/cli/commands/app/init.test.ts to use real temporary directories via inTemporaryDirectory instead of mocking @shopify/cli-kit/node/fs.

How to test your changes?

CI

Checklist

• I've considered possible cross-platform impacts (Mac, Linux, Windows)
• I've considered possible documentation changes
• I've considered analytics changes to measure impact
• The change is user-facing — I've identified the correct bump type (patch for bug fixes · minor for new features · major for breaking changes) and added a changeset with pnpm changeset add

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PR created automatically by Jules for task 9629675890244724247 started by @gonzaloriestra

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