Examples need some polishing

In the past few weeks, I have tried running some different scenarios for benchmarking purposes and I realized that the examples need a bit of updating so they include electromagnetic interactions out of the box and maybe a more general environment that includes a refractive index profile.

Finally, in the vertical_EAS.cpp example there is a misuse of the endOfShower() / startOfShower() which causes it to write an extra "null" shower.