class RuboCop::ConfigLoader

def merge_with_default(config, config_file)

that only cops from user configuration are enabled.
AllCops:DisabledByDefault is true, it changes the Enabled params so
Merges the given configuration with the default one. If 
def merge_with_default(config, config_file)
  configs =
    if config.for_all_cops['DisabledByDefault']
      disabled_default = transform(default_configuration) do |params|
        params.merge('Enabled' => false) # Overwrite with false.
      end
      enabled_user_config = transform(config) do |params|
        { 'Enabled' => true }.merge(params) # Set true if not set.
      end
      [disabled_default, enabled_user_config]
    else
      [default_configuration, config]
    end
  Config.new(merge(configs.first, configs.last), config_file)
end