Properly use CommandLineArgs class for options parsing in examples
Currently some (or all?) examples use the CommandLineArgs class to parse the CLI parameters, but they do not pass the parsed options to the simulation. Also the CommandLineArgs class is very inflexible, e.g., it does not allow string options.
Maybe its a good idea to leave option parsing to internal components such as the different solvers rather than doing it centrally where it is not properly maintained.