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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: I2b2fb4c746fa26097110f08d211c28076fd81942

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: I5257228912bbf3d8e1228ead4d2a0910f1e2da6b

Change-Id: Ic7cca995e793691c508b1db5c8ee8f649622a616

Change-Id: If1dbd844c06e3c4ffa53c4e1691bb8c7ecb510aa

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

Change-Id: I1c0ed174ff576ea23b3adbb2235a17a1014e3859

Change-Id: I1fb5685cd9e923ea91e0a5c55a90e68d93f4c4ef

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

Adding lp suspend for wait operations in MPI Sim layer, adding commit_f in dumpi workload debug utility

Bug fix in dfly routing

Change-Id: I53f278953f2e287bf122cf20694a7db3bd1fd336

See merge request !7

Change-Id: I53f278953f2e287bf122cf20694a7db3bd1fd336

Slimfly LP-IO Update

Fixed issue #152 .
Updated Slim Fly workload README accordingly

See merge request !6

Commit function

The ROSS API has changed to add a commit function (see [d3bdc07](https://github.com/carothersc/ROSS/commit/d3bdc077a0c4d1481dc06c4b4d4f1eb8e4e6fbf6)).

This merge request updates the various CODES models to the latest ROSS API. All  test pass. It also updates the documentation to CODES v 0.5.2 and ROSS v d3bdc07. 

See merge request !5