Added flush statements and clarified restart comments

I have added some flush statements that make sure that the screen output of the test cases is printed in the corrected order. Before it was very unclear which output belonged to which case, so this is now fixed. I have tested the new output here: https://gitlab.windenergy.dtu.dk/EllipSys/ellipsys3d/-/jobs/5020 (Ignore the segmentation error.)