proto_generator may generate duplicate messages with package_hierarchy=true

[tokarenko]

Issue description

proto_generator incorrectly processes IETF interfaces YANG model and generates duplicate InterfaceKey message at top-level ietf_interfaces.proto.

Steps to reproduce:

1. Launch proto_generator as follows:
   proto_generator -output_dir=./proto -package_hierarchy=true ietf-interfaces@2018-02-20.yang ietf-arp@2019-11-04.yang

2. Obtain unexpected duplicate InterfaceKey message in generation result in ./proto/openconfig/ietf_interfaces/ietf_interfaces.proto

// openconfig.ietf_interfaces is generated by proto_generator as a protobuf
// representation of a YANG schema.
//
// Input schema modules:
//  - ietf-interfaces@2018-02-20.yang
//  - ietf-arp@2019-11-04.yang
syntax = "proto3";

package openconfig.ietf_interfaces;

import "github.com/openconfig/ygot/proto/yext/yext.proto";
import "openconfig/ietf_interfaces/interfaces/interfaces.proto";
import "openconfig/ietf_interfaces/interfaces_state/interfaces_state.proto";

// InterfaceKey represents the /ietf-interfaces/interfaces/interface YANG schema element.
message InterfaceKey {
  string name = 1 [(yext.schemapath) = "/interfaces/interface/name"];
  interfaces.Interface interface = 2;
}

// Interfaces represents the /ietf-interfaces/interfaces YANG schema element.
message Interfaces {
  repeated InterfaceKey interface = 398263028 [(yext.schemapath) = "/interfaces/interface"];
}

// InterfaceKey represents the /ietf-interfaces/interfaces-state/interface YANG schema element.
message InterfaceKey {
  string name = 1 [(yext.schemapath) = "/interfaces-state/interface/name"];
  interfaces_state.Interface interface = 2;
}

// InterfacesState represents the /ietf-interfaces/interfaces-state YANG schema element.
message InterfacesState {
  repeated InterfaceKey interface = 199470812 [(yext.schemapath) = "/interfaces-state/interface"];
}

Expected result

Expected result is that InterfaceKey is not duplicated.
proto_generator works as expected with nested messages (without -package_hierarchy=true).

message Interfaces {
  message Interface { 
    ...
  }
  message InterfaceKey {
    string name = 1 [(yext.schemapath) = "/interfaces/interface/name"];
    Interface interface = 2;
}
  repeated InterfaceKey interface = 398263028 [(yext.schemapath) = "/interfaces/interface"];
}

message InterfacesState {
  message Interface { ...
    ...
}
  message InterfaceKey {
    string name = 1 [(yext.schemapath) = "/interfaces-state/interface/name"];
    Interface interface = 2;
  }
  repeated InterfaceKey interface = 199470812 [(yext.schemapath) = "/interfaces-state/interface"];
}

Supplementary information

Contents of ietf-interfaces@2018-02-20.yang

  container interfaces {
    description
      "Interface parameters.";

    list interface {
      key "name";

...

  container interfaces-state {
    config false;
    status deprecated;
    description
      "Data nodes for the operational state of interfaces.";

    list interface {
      key "name";
      status deprecated;