1) Adding meshset argument for some important functions in ParallelComm and Skinner.
2) Do not assume a default root set (=0) unless explicitly necessary.
3) As we move towards loading more meshes together (MBCoupler) using file_sets, dealing with root_set alone is problematic.
4) Fixed all other examples and tests to follow the new API.
5) Removed some shadow warnings in some source files.