MergeJavaResource fails because of duplicate .proto files

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.