This diff introduces changes to unify source paths according to the repository. These changes are required to remove the conditional paths includes in CMake and simplify future includes into the Cargo `build.rs` file as long as unifies the directory structure.
This diff also includes some minor prettifying to the `CMakeLists` and `Dockerfile`.
Related Linear task: [[ https://linear.app/comm/issue/ENG-2044/fix-compiling-of-protobuf-file-in-cargos-buildrs-in-docker-for | ENG-2044 ]]