More general implementation of non-simply connected domains

[CsatiZoltan]

When a large grain contains one or more grains, the large grain has to be modified to exclude the small grains that act as holes. This makes the large grain a non-simply connected domain.
This modification can be carried out as

• Boolean operation (set difference)
• boundary representation

Currently, I plan to support the Boolean solution for the splinegon representation only, as that's what I actively work with. However, a general implementation would be nice, which does not need to have information about the actual geometrical representation. I.e. it would work for the polygon representation too. That would however require several changes in the code:

• The cad module would import the geometry module for the sake polygon-based operations.
• The region_branches variable will no longer be a simple list, but a list of lists in order to incorporate the holes
• The geometry.Polygon class must be modified so that holes can be represented, which needs
  • updating the methods for calculating the area, the equivalent diameter, etc.
  • the data structure will not remain a simple nx2 NumPy array, but a list of NumPy arrays, that describe the outer boundary and the internal boundaries as well