Merging most recent changes into main branch - Settings class, Command line support, Mapupdate and Mollification

[Arcadia197]

I am now merging all most recent changes onto the main branch. This includes a big list of changes, most importantly:

• creation of settings class which hosts most of the important settings, a lot of settings have been moved here
• support of setting variables at command line level
• introduction of higher order map update stencils
• introduction of mollification
• merge of map advection and map update

more details in each linked commit