changed MPI_COMM_WORLD into MPI_COMM_CODES and made model-net-mpi-replay a function instead of a main

Updating dragonfly model to take into account multiple links connecting the chassis, updating config files and workload generator as well

Preparing beta version for new dragonfly model, modifications to routings, adding documentation for generating config files, adding libtools to support C++ code compilation

Adding first pass of dragonfly custom model: routings (adaptive, progressive adaptive, minimal, non-minimal) should be functional with DF traces, need to update for making optimistic mode functional

Change-Id: I1c491d4c9003f6a79aff42ffe7fc9f5bbb64a0cc

Change-Id: Ic7cca995e793691c508b1db5c8ee8f649622a616

Change-Id: If1dbd844c06e3c4ffa53c4e1691bb8c7ecb510aa

Add static to many functions that don't need to be visible.

Change-Id: I1c0ed174ff576ea23b3adbb2235a17a1014e3859

Change-Id: I4e6919802940df120b87ff4c709d3825993373ac

updating MPI sim layer for blocking receives, updating dragonfly model for the message remainders, checking for negative byte size in dumpi traces

Change-Id: I53f278953f2e287bf122cf20694a7db3bd1fd336