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Re-factor main() so that all options are handled by new class CcsmOptionsHandler
Re-factor existing classes so that const reference to options object is used & retire macros SHOULD_INCLUDE_FUNCTION, etc.
Fully encapsulate all options into MetricOptions class
Currently analysis of c++ code is not supported. Until it is, a warning or error should be issued in the case that c++ code is fed into CCSM.
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