Fix a bug in calculating root respiration. The bug is root

respiration doesn't include the live coarse root maintenance
respiration. It should include the livecroot_mr according to the tech
note. See the fixation in src/biogeochem/CNVegCarbonFluxType.F90.
This change happened after the assimilation and free runs were
completed.

This adds in some changes that may be roundoff different in preparati…

…on for bringing in the changes

that allow turning on the bio-mass heat storage option. There's a few zeroed terms added to some calculations
in CanopyFluxes. The new terms are identical to what will come in for BHS except the zeroed terms are
not arrays here but scalars. I showed the new terms are only off by roundoff with a previous commit that added
explicit tests for the terms and verified it for two tests.

Fix ndep from coupler

There was a bug in ndep forcing (forc_ndep_grc) when receiving ndep from
CAM (ndep_from_cpl true). This first appeared in ctsm5.1.dev002. NDEP
forcings have been garbage since then when receiving ndep from CAM.

This tag fixes that issue.

This api update includes new history dimensions added by Greg Lemieux

Incorporate changes from ctsm1.0.dev110

Incorporate changes to ncdio_pio.F90.in and histFileMod.F90 from
ctsm1.0.dev110 (ESCOMP#1095).

I'm not sure why I didn't include these changes on this branch
initially; my best guess is that I just forgot about them.

Add ACTIVE (T/F) column to master hist fields table and alphabetize

Write history fields master list to separate optional file

User can choose to write the history fields master list in a separate
text file by setting hist_master_list_file = .true. in CTSM's namelist.

File contents follow recommended reStructuredText "simple table"
formatting (see
https://docutils.sourceforge.io/docs/user/rst/quickref.html#tables)
for use in CTSM documentation in the sphinx environment.

Various updates needed for NUOPC

Also adds mizuRoute as an external component

A few small fixes

(1) Fixes needed for PIO2 when running in pts/scam mode (from Jim
    Edwards and Bill Sacks)

(2) Fix mpi broadcast of hist_avgflag_pertape so that this namelist
    variable is applied properly (from Sunniva Indrehus, Keith Oleson
    and Bill Sacks)

(3) Fix invalid xml in namelist_definition_ctsm.xml

(4) Add point of interest code for debugging

Fixes to pio_get_var for single_column mode, needed for PIO2