updated comments with directives.  However - left transaction related comments alone becuase they will be overwritten with changes/new-improved comments in my transaction class refactor which is nearly done.
moved logger doc from class file to site.
I read, tested, and ran a number of the standard input files against this change. I made some general style comments, but it looks good. Thanks for complying.
Merge branch 'develop' into cleanups
updated cli usage help output to clarify verbosity arg
reinstantiated some adjustments overwritten in merge.
cleaned up includes in message class.
added include so converterModel no longer 'borrows' the include from Message.h
created transaction class and moved trans-related methods out of Message class and into Transaction class.
got rid of transaction static factory methods - they were a bad idea.  Added a TransType enum.
much progress converting existing models to use the new Transaction class.
more work converting models to use new transaction class.
Eliminated some code duplication in RecipeReactor.  RecipeReactor updated to use new Transaction class.
added clone method to transaction class - used by Message class clone method.  Remaining models configed to work with new transaction class.
transaction market() method has code that makes it clear that it throws an exception.
renamed somVars to some_vars and cleaned up/improved comments with directives.
Merge pull request #144 from rwcarlsen/logger-doc

moved logger doc to site and improved cli usage help
This removes the repository input files from the core. They're not supposed to be here.
Merge pull request #149 from katyhuff/input_cleanup

Input cleanup - Katy's workspace
Pulled and tested, This fixes #102 .