Refactor of fire code vector indices, fixes to logging

This set of changes contains a set of updates to the fire code, which makes the indexing of litter pools match indexing in relevant non-fire vectors of the code. This set also contains important bug fixes in the logging module.

Note that index changes in the fire code will impact users, in that the values in the parameter files have not changed order for the following variables: fates_FBD, fates_low_moisture_Coeff, fates_low_moisture_Slope, fates_max_decomp, fates_mid_moisture, fates_mid_moisture_Coeff, fates_mid_moisture_Slope, fates_min_moisture and fates_SAV. Specifically, index 1 of the parameters has now been moved to the last position, and the other positions have been moved to lower positions. See differences here: https://github.com/NGEET/fates/pull/523/files#diff-a236898dbb7848d5cfdf2610b0ba32c0R1124