Adding sampling examples in synthetic workload test program, fixing a reverse handler bug in synthetic workload test

Fixing the contiguous memory allocation bug with dragonfly router sampling, sampling struct had two dynamic arrays so a contiguous fwrite wasn't working

Adding sampling for dragonfly routers (in progress), updating binary read file utility to read router samples

(i) Adding sampling for dragonfly compute node LPs (ii) Adding file I/O reader that translates the binary format to text

NOTE: no models implement it yet

Build system and documentation files were largely hand-merged.

(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

Updating the network model documentation, added examples on how to run network models with dumpi traces, fixed comm time in MPI Sim layer