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Currently, it is required for some options to be explicitly declared in the configuration file.
In theory, all default configurations are set by calling CreateDefaultConfig but unfortunately, the subtree extraction (e.g. performed for sending configuration to workers) does not extract these values.
I opened a bug in the upstream repository of viper: spf13/viper#747
For now, I recommend to simply use the complete configuration file as delivered with nray and enable/disable modules manually.