if the OF end time gets modified at runtime, we need to update the time
setting for invoking the write_restart command if we only want to write
at the end of the simulation;
otherwise we will either write the file too soon or - probably even
worse - not at all
Done away with awful creation of sub-directories for the derived classes of "liggghtsCommandModel"
Followed standard OpenFOAM convention, which can be seen all-over OpenFOAM's sources.
Also fixed some parameter reading from the sub-directories.
