Update npm lockfile to version 3 format

npm versions >= 9.x natively use lockfile format version 3. We expect the users will use the version of npm that is
bundled with Node.js and the project uses Node.js 20.x, which bundles npm versions >= 9.x. So it will be useful and
appropriate to use lockfile version 3 for the project.

This change does result in a loss of compatibility with npm version 5.x and 6.x, but we do not support use of that npm
version with the project anyway.

The `dependencies` object was solely present to provide backwards compatibility npm versions that used the lockfile
format version 1 (npm 5.x and 6.x), so it is intentionally removed as part of the migration to lockfile format version
3.