Update code base and documentation after proto files generation refactoring

After the refactoring done as a part of KOGITO-4073, the proto files are no longer present under target/classes/persistence and there is no need to copy them to the Kogito service image. Also kogito-application.proto file is no longer being generated. However, there are still some leftovers in the kogito-cloud-operator and in the kie-docs making use of this location.