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

Change-Id: I2d673f6b4925e97efd79f3e383607068914cf78e

Adding updated allocation generator script (uses random number seeds for multiple allocation files), torus cleanups

NOTE: no models implement it yet

(i) more text on how to run dragonfly with network traces (ii) some stat reporting fixes with dragonfly (iii) modifying config file error handling for dragonfly/torus (iv) modified dragonfly reverse handler for out of order packet handling, now it deletes the hash entry that it created in forward mode

Torus model revision: adding bubble flow control for deadlock prevention and updated congestion control

NOTE: caused an event size bump - you may need to update config files

Updating torus network model: now generates one chunk at a time and holds off another until the previous one is sent