[Tests] Remove filesystem mocks in execute-command-helpers.test.ts

[gonzaloriestra]

WHY are these changes introduced?

The tests for prepareExecuteContext were using filesystem mocks, which test implementation details (that certain functions were called) rather than behavior (that the query is correctly read and validated).

WHAT is this pull request doing?

Refactors packages/app/src/cli/utilities/execute-command-helpers.test.ts to remove the global mock of @shopify/cli-kit/node/fs. It uses inTemporaryDirectory and writeFile to create real files for testing the --query-file flag logic.

How to test your changes?

CI

Post-release steps

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 4749985076809950236 started by @gonzaloriestra

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