Fix uninitialized rxfire_area_fi and rxfire_area_fuel

Refactor initial seed parameter into two new parameters

This creates a new parameter `fates_recruit_init_dbh` to set the initial
seedling DBH.  Prior to this tag, `fates_recruit_init_density` could
enact this functionality by setting a negative value.

Complete the FATES-CLM nitrogen coupling on the FATES side

PR #1472
PR not yet merged on the CLM side: ESCOMP/CTSM#3409
Issue ESCOMP/CTSM#3378

Adding lupft seed bank diagnostics, and conflict resolution with noresm

Updates to the grazing logic

This prevents crop and simliar being grazed to death in the off-season

 Update check for missing values in incoming datasets

The land use timeseries and luh x pft mapping data checks have been
updated to handle NaN or -999 values for netcdf _FillValues

Fixes were applied to biomass by Jessie Needham

Land use clearing logic update

This update allows the user to select the logic option that defines
whether or not to kill vegetation during land use transitions.

Fix to infinite loop in the damage code.

Fixes to initialization of cohort mean vcmax 25 when no leaf biomass …

…is present.