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chore: @npmcli/package-json refactor

Refactor set-script and init to use @npmcli/package-json as a uniformed
way to update and save package.json files.

Fixes: https://github.com/npm/cli/issues/3234
Relates to: https://github.com/npm/statusboard/issues/368

PR-URL: https://github.com/npm/cli/pull/3455
Credit: @ruyadorno
Close: #3455
Reviewed-by: @nlf

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