for example, if my github repo is project.git and my structure is project/utils/tool.py

You can't, since the repository is cloned to an ad-hoc location (not a fixed location). The best thing to do is use local imports (i.e. import sibling modules)

Hi BoredHedgehog47 , what import errors are you getting?

hmm how would I add that to PYTHONPATH? Can that be done in the SETUP SHELL SCRIPT window?

I'm getting import errors when I do, from project.utils import tool all from the working directory of project

they are pathing errors to in my repo

I don't think you can import from you project as it is not part of the pythonpath