Produce new mat-end subtracting existing conditions

Gives the option to produce new conditions after subtracting the current conditions, or relative to the existing conditions, as required.

New default is to produce new conditions after subtracting the current conditions.

This change is required as it was previously thought the values would only need to be calculated once, but now they are recalculated in iterations of the alignment

Also now calculates the residual wrt the (weighted) average residual of the mat