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fix(config): consolidate use of npm.color

The config value for `color` should never be directly read by npm, or
its submodules.  The derived value `npm.color` or
`npm.flatOptions.color` is what we want to use.

This PR consolidates the use of these values, makes sure there is only
one place the value is actually calculated, and stops relying on
duplicated code in the setup-log.js file for setting one of them.

PR-URL: https://github.com/npm/cli/pull/3563
Credit: @wraithgar
Close: #3563
Reviewed-by: @lukekarrys

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