Make Exodus reader respect the numbering in node_num_map.

Miscellaneous changes/improvements:
* Asserting mesh.n_nodes()==num_nodes is no longer valid if the nodes do not
  form a contiguous numbering starting from 1.
* Set correct, mapped node pointers when building Elems and creating nodesets.
* Write out node_num_map from write_nodal_coordinates function.
Minor code cleanup and reformatting.
Merge branch 'exodusII_node_map'