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Refactor and simplify the core config module (#2945)

This PR is a refactor of the core config module. The main issue fixed is that there was no way outside of the `with clause` method to alter a modules default configuration. Changes in this PR ensure that when using the `config.set` mixin, the values set now *replace* instead of *merge* the default value provided by a given module.

**Related changes include:**

- `config.apply` has been renamed to `config.merge-with-default` which makes the mixin's intent more clear.
- Contents of the `core/config` docs page have been updated to reflect these changes.

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