Replace base mixins by PorePyModel as base class in porepy-provided simulation set-ups

[vlipovac]

There are classes inside porepy which provide concrete set-ups for boundary conditions and md-grids for example.

As of now, some of them inherit directly from the respective mixins, which they should not in order to avoid MRO issues in the mixin framework.

Primarily affected are

• porepy/applications
• porepy/examples

A check whether other files/classes are affected should be carried out as well.

Fix:
Replace the mixins by the recently introduced PorePyModel protocol class, which suffices to provide an interface to the methods required from the mixins.
Make sure that no untyped code or code which cannot be picked up by linters, results from above changes.