Calibrating the magnetometer with linear algebra

Is there a procedure to upload an app to the espruino repository?

Not particularly, no - just fork https://github.com/espruino/EspruinoApps and make your changes, and make sure there's a green tick next to your commit (which shows that the checks succeeded - if it's a cross just click on it to find out what failed). After that it should be easy to submit a PR