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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

Change-Id: I2d673f6b4925e97efd79f3e383607068914cf78e

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

-- Make all functions static
-- Bug fix in packet_arrive
-- Change ts calculation in packet_send

Change-Id: I2bba1c074ebf0dc641ca025916d9a689d4807731

- Fat Tree readme now includes documentation for the custom- "pruned"
fat tree layout which is used to create the Summit network.

Documentation in src/networks/model-net/doc/README.fattree.txt

This commit is joint work by Jens Domke and Nikhil Jain.

Jens did all the ground work for dumping the topology and reading the routing
tables. He also wrote the scripts that perform the intermediate steps that
generate the routing tables using the topology.

Nikhil integrated Jens's changes into CODES by breaking them into a 3 step
process as described in src/networks/model-net/doc/README.fattree.txt.

Change-Id: I1478fb2ab83b9ded0673d8f897e09a423868795a

- Update routing algorithm to take into account new custom- mapping
between L1 and L2 switches
- Added total finished packets to stats collection file
- Updates to layout connections output for visualization

 - Verified to construct 3-level fat trees correctly using custom-
approach.
 - Verified to work with 2, 3 and 4 pods.

Fixing memory leak in checkpoint restart workload, Merging Nikhil's suggested changes in dragonfly with some fixes

 - fattree-config-up-connections
 - sim_log.txt