Moved polarization check to DWBASimulation and added a matrix-valued output data structure there to hold polarized scattering data

Conflicts:
	App/src/FunctionalTestFactory.cpp

Manual - example - updates for particles (refractive index replaced by material manager with mParticle)

Manual - Example - Implementation of Gennady's comments (new figure for sample, \alpha_0 \phi_0 replaced by \alpha_i,  \phi_i, remove identical remarks, url of NumPy moved to references)

Conflicts:
	Doc/UserManual/Examples.tex

Conflicts:
	Doc/UserManual/UserManual.pdf