Yes, the generated schema will contain Dgraph directives like @generate and @search .
Why do you need to remove Dgraph directives like @search and @generate. I do understand that they are Dgraph specific and may not add value while using the schema with other tools. But, my understanding is that they are harmless and don’t need to be removed while using with other tools like Apollo Federation.
We can look into having an endpoint with removed Dgraph specific directives if there is a valid use case for it.
Also linking a somewhat related post for reference.