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chore(refactor): finish passing npm context

No more requiring npm as a singleton.  This will now allow us to move
forward with the other refactoring we need to always use the npm object
itself in tests, not a mocked one.

PR-URL: https://github.com/npm/cli/pull/3388
Credit: @wraithgar
Close: #3388
Reviewed-by: @ruyadorno

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