refactoring embedded entities: now only in GModel

Geo/GModel.cpp

Geo/GModelFactory.cpp

Geo/GModelIO_GEO.cpp

Geo/GModelIO_GEO.h

Geo/Geo.cpp

Geo/Geo.h

Geo/discreteDiskFace.cpp

Geo/discreteEdge.cpp

Geo/discreteFace.cpp

Geo/discreteRegion.cpp

Geo/gmshFace.cpp

Geo/gmshRegion.cpp

Parser/Gmsh.l

Parser/Gmsh.tab.cpp

Parser/Gmsh.tab.hpp

Parser/Gmsh.y

Parser/Gmsh.yy.cpp

Parser/Parser.h

Plugin/FaultZone.cpp