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fix: shrinkwrap setting incorrect lockfileVersion
Fix: #3962 When created from a hidden lockfile, shrinkwrap was always setting the lockfileVersion to 3. The shrinkwrap command also needed to be updated to log the correct message based on the lockfileVersion config instead of the static lockfileVersion. With these fixes, it was possible to log a better message whenever we are changing the lockfileVersion, either from a config or any existing lockfile. Lastly, the tests for shrinkwrap were completely refactored to use the real npm and test all conceivable scenarios, as well as removing usage of `util.promisify` in favor of `fs.promises` now that we've dropped support for Node 10.
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