Cleanup

This is based on the devel_rogue_test branch from @wittgen , but extends on the restructuring:

• fully move to cmake, remove existing make file
• move compilation from sub folder to root folder
• move some files around to adapt to the new root folder

@bgallop Could you please crosscheck my changes and let me know what you think. This also does not use your container, should we correct that?

@jolamber @mtrovato Could you guys crosscheck if this works with FELIX? This uses a fully contained build (Does not include all the fixes from the other branches yet, but should be good enough to test)