Global configuration file merged with project configuration file

I'm trying to use the python language server, pyls-mypy and mypy to asynchronously show me type hints in vim.

This is a bit related to #4542 and #5241.

Immediately I had the problem of Cannot find module named 'a.b.c' which sent me down a rabbit whole trying to figure out what to do. It seems like the answer is --ignore-missing-imports. Since I'm not invoking mypy myself I would like to put this information in a config file. So I put it in ~/.mypy.ini and the error message does not go away. Finally I figured out that setup.cfg is shadowing my configuration file, and yes, putting the [mypy] block in the setup.cfg finally let's me get rid of the warning.

So my question is. What is the proposed solution to get rid of this warning for all my python projects? My preferred solution would be that any project-local configuration file is merged with my personal configuration file (like other tools would do, e.g. git and pylint).

No files, tests, or entry points are named. Start by tracing how mypy discovers and prioritizes ~/.mypy.ini and project setup.cfg, then review the related issues #4542 and #5241. Done means defining and implementing clear merge behavior so personal configuration can apply across projects without losing project-local settings.