Ensure `uv run eest make test` calls `ruff` and formats the generated test module correctly

`uv run eest make test` runs correctly, but the generated test module is not correctly formatted.

From the copilot review:

The code now references `AppConfig().ROOT_DIR.parent` instead of `AppConfig().ROOT_DIR` to find pyproject.toml. This change suggests the ROOT_DIR definition may have changed during the refactor. Verify that ROOT_DIR still points to the correct location (packages/testing/src/execution_testing) and document why .parent is now needed.
```suggestion
# Call ruff to format the file
# AppConfig().ROOT_DIR points to 'packages/testing/src/execution_testing'.
# The project's pyproject.toml is located in the parent directory: 'packages/testing/src'.
# Therefore, we use .parent to correctly reference the config file.
```

_Originally posted by @Copilot in https://github.com/ethereum/execution-specs/pull/1654#discussion_r2459545228_