Removed items are kept in overridden configuration

When updating domain overridden configuration data, we are currently merging the original override data with the newly submitted data using the Drupal NestedArray::mergeDeepArray method.

This is problematic as the merge is keeping items that are supposed to be removed.

The solution is to simply use the moduleOverrides property to store the updated data instead of using a custom property and merge them.

Note that configuration items provided by the base configuration will continue to apply unless they are explicitly overridden in the domain-specific configuration.

If you do not want an item to appear in domain overrides without explicitly overriding it, you need to remove it from the base configuration.

Another point to keep in mind is that when configuration overrides are merged, the order of items can change: items not present in the base configuration are appended after the base ones, since the base configuration is loaded first.

An example of such a problematic configuration is language.types, which is used on the language negotiation configuration page.

The LanguageNegotiator getEnabledNegotiators method expect the enabled negotiators to be available in the right order in the configuration. It might not be case anymore if the configuration has been overriden.