Simulation: do not use global instance of ConfigFlags, part 1

This is a first of series of MRs to drop the global instance of ConfigFlags. It introduces initConfigFlags function (renamed existing function) which should be imported in tests and skeletons. Also all instances of ConfigFlags arguments or local variables will be eventually renamed as they do not really comply with coding standards (arguments and local variables should not start uppercase).

This MR starts with a part of Simulation which is not wrapped.

Tagging more people the first time: @jchapman, @tlari, @mbandier, @fwinkl, @wlampl, @christos, @mhodgkin, @jcatmore, @nstyles, @tstreble