Standardize NBE and NEE throughout CARDAMOM code

[aantonyb]

Some ambiguity within code as to what is NEE and NBE.
To do: define exactly how fire and methane are treated in NBE.
To do: define NBE as "CO2 only" flux, or "total C" flux? Recommend or acknowledge limitations.
Solution = define in manual + change across all CARDAMOM code
Follow branch + merge strategy (as outlined in manual)

[aantonyb]

Done in observation operator branch. All references are to NBE. approach allows for easy incorporation of new observation operators, eg NEE or NBE (co2 only) as and when needed