Fix loading empty properties by CLI json parser.

[BarkingBad]

The problem was when we used DokkaSourceSetImpl as TypeReference for Jackson object mapper, we could end up with an error:

Exception in thread "main" java.lang.ClassCastException: kotlin.collections.EmptyList cannot be cast to kotlin.collections.MutableList

The issue stems from the default implementation of DokkaSourceSetImpl, that if there is no such property in json, it was returning EmptyList which cannot be cast to MutableList in case of mutating its state for CLI with global options purposes #2292 . The same problem applies to Sets