Single configuration function to be called from Allen.cpp and RunAllen.cpp
At the moment, locations of some parameters (such as the Kalman filter parameterization) are coded in two places in Allen: once for standalone execution (https://gitlab.cern.ch/lhcb/Allen/-/blob/master/main/src/Allen.cpp#L450) and once for calling Allen from Moore (https://gitlab.cern.ch/lhcb/Allen/-/blob/master/Rec/Allen/src/RunAllen.cpp#L78).
This should be done in a single function called from both Allen.cpp and RunAllen.cpp