MergeJavaResource fails because of duplicate .proto files

[ADVavvas]

There are 3 modules in the project: app, app-common, app-native.

• app-common is a Java module that contains the .proto classes that get compiled to Java. Both other modules will depend on the Java classes.

• app-native is an Android module that contains a C++ library that also needs to compile the same .proto classes but in C++ (and also depends on the Java classes).

• app depends on both.

At the moment, since app-native requires both Java and C++ compiled protobuf classes it declares 2 dependencies:

implementation project(path: ':app-common') // Java dependencies
protobuf project(path: ':app-common') // .proto files to be recompiled but in C++

This leads to duplicate .proto files when merging:

> A failure occurred while executing com.android.build.gradle.internal.tasks.MergeJavaResWorkAction
  > 2 files found with path 'Foo.proto' from inputs:
     - /Users/..../app-native/build/intermediates/library_java_res/debug/res.jar
     - /Users/.../app-common/build/libs/app-common.jar

Adding packaging options to app-native e.g. resources.excludes.add("*.proto") seems to have no effects.
Excluding the .proto from app-common (jar { exclude '**/*.proto') somewhat works for the user defined protos, but still fails with the same error caused by google/protobuf/Foo.proto` instead.

I realise the project configuration might be unconventional but I don't know what an alternative could be, so any help is appreciated.