the remaining Doxyfiles write to subdirectories html/std, long, dirgraphs

New doxygen docs switched on, Doxyfile.in is introduced for automatic propagation of version number in the project.

MesoCrystal test is off, new fitting examples for spheres in a lattice and corresponding changes in visitors

On the way to add roughnesses of layers: new classes IRoughness, LayerInterface, lots of comments and const references. New Doc/Doxyfile for oxygen generation.