[GeoMechanicsApplication] Move utility functions for element matrices to the element level

[rfaasse]

As a developer, I want to have the element matrix utility function to act on an element level instead of an integration point level, such that the code is more readable and it is possible to integrate the utilities into our strategy architecture (see #12318).

Acceptance Criteria
The created utility functions CalculatePermeabilityMatrix, CalculateCouplingMatrix and CalculateCompressibilityMatrix calculate the contributions for all integration points at once

Predecessor #12319

[rfaasse]

For this issue to be implemented satisfactory, we need to reduce the duplication of CalculateAll, or ideally remove it altogether first.