With this, almost all directories have unidirectional include dependences

As recommended by
https://google.github.io/styleguide/cppguide.html#The__define_Guard

Co-Authored-By: Walter Van Herck <walter.vanherck@gmail.com>

Previous implementation provided wrong number of elements in
the intensity map for off-spec simulation. In the case of GISAS
it has skipped masked areas

Simulation::numberOfSimulationElements was previously used as a synonym
to the number of values in the intensity map. However it is different
in the case of SpecularSimulation with beam divergence and could lead
to malfunctioning in the future. To avoid confusion,
numberOfSimulationElements method was placed in the
protected scope of Simulation class. Simulation::intensityMapSize returns
the actual size of intensity map.