In general, I’m trying to create a readable configuration file and a state of the application at the same time. It looks like all this data is only neccesary in the unexported application, isn’t it? Can some or all of this be omitted? It would have been enough, just to remove the assembly part I think.
You probably should use the vvvv XML serializer, not the Binary or JSON serializer. Then the serialization should look much simpler. You can still convert the XML to JSON if you want to.