Remove hardcoded MPI_COMM_WORLD in QUESO

For #72-- this removes all but one reference of MPI_COMM_WORLD from QUESO.  Detailed below. 

1) Removed severals references to MPI_COMM_WORLD when RawType_MPI_Comm was intended instead. 

2) On line 1221 of core/src/Environment.C there was an explicit call to MPI_COMM_WORLD. This was harmless but removed. We should not assume we have access to MPI_COMM_WORLD. 

3) Found a subtle bug in Defines.C this method is suppose to return the rank of the calling process in the communicator. However, it is hard coded to return the ranks in MPI_COMM_WORLD. Again, if the communicator is NOT MPI_COMM_WORLD, this will return an incorrect number of tasks. 

However, this has not been fixed. The defines.{c,h} files do not need to know the Queso environment. Instead, let's deprecate the entire UQ_*_MACRO calls, and replace with queso_exit(). This knows how to handle parallelism implicitly. This will be the subject of another ticket.