Rework config file and command line argument substitution
It is possible to specify a config file and further command line arguments that replace variables set in the config file, allowing for parameter studies with the same config file. See core/Environment.h and core/config/Create.h.
However, the documentation is misleading (which order should there be: "configFile var1 var2" or "var1 var 2 configFile").
Also, there seem to be two replacement mechanisms:
Directly in the create function (Create.cpp) via
config->addValueReplacement( &argv[i], argv[i+1] )
and then in the later called function
substituteCommandLineArgs( *config, argc, argv )
Both seem to require differently formatted command line arguments. Also, it seems ambiguous to have two mechanisms achieving the same thing.