Major API change

* Problem: We needed a way to read in the matrix into a Matrix
  datastructure in addition to building the graph. This has multiple
  reasons:
  1. We may need to compute the compressed matrix using the input
     matrix.
  2. We need to obtain the number of rows of the input matrix to
     generate the seed matrix.
* This required major API changes, mainly the split of IReader's Read
  into ReadGraph and ReadMatrix
* I was able to avoid major code duplication in MMReader, nonetheless:
  The file is currently a mess that uses many shortcuts and is generally
  unclean