#1210 Increase the use of InitMoReFEM, rebranded MoReFEMData

Now for instance Model constructor takes one MoReFEMData parameter, rather than Mpi and InputParameterList.

This streamlines the interface and group together the variables that are almost global ones.

The incentive to do so was the management of output directory: for the external hyperelastic model, same Lua file could be used for different cases, and we would like to make the result directory differ. The new class is the most pertinent location for the extended output directory.