How to manage both python project and c++ project under the same git repository?

Hi, 

I have a project which is written in python and c++, I pycharm to develop the python code base and use clion to develop the c++ code base. It worked well when I have 2 individual git repositories under github.

Now I have a lot of c++ code generated by my python code, so these 2 projects become highly dependent. It makes more sense now to put them under one single git repository, so when I can tag and release them together.

however, pycharm and clion both are based on the assumption of single dedicated git repo: when I add the 2 projects together, they start to conflict with each other.

Does anyone has the same problem? how do you resolve this?