This code should be moved in Factory::createComposer because otherwise it's bound to create weird side effects at some point.

Now whether to use array_replace or not I'm not sure. I'd say it's probably enough for most things, but maybe for config or require it'd make sense to do an array_replace *within* the key? Maybe we should do it for all top level keys, so sort of recursive but not all the way, just array_replace per key if it's an array on both sides, and otherwise override it if it exists in the $parsed array here.