[Tests] Refactor theme-command.test.ts to use real temp dirs

[gonzaloriestra]

WHY are these changes introduced?

Following the testing protocol to replace filesystem mocks with real temporary directories for better test reliability and isolation.

WHAT is this pull request doing?

• Refactored packages/theme/src/cli/utilities/theme-command.test.ts to remove vi.mock('@shopify/cli-kit/node/fs').
• Introduced a withThemeEnvironment helper to wrap tests in inTemporaryDirectory and mock cwd() to point to the temp dir.
• Updated all mock command classes to use the dynamic cwd() for default flag values.
• Ensured full test coverage is maintained by restoring all assertions and test cases.

How to test your changes?

CI

Post-release steps

N/A

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 12932754602815531784 started by @gonzaloriestra

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