restart fix for efflux variables

[rgknox]

Description:

Efflux is defined at the cohort scale. Efflux is passed from the cohort to the output flux to the HLMs litter pool before we perform disturbance and mortality. Thus, in order for restarts to work, this flux at the site level must be preserved prior to mortality and disturbance. Luckily, we can use the flux_diags structure which already exists to generate the output flux, this same flux will be preserved after a restart read.

Fixes: #763

Collaborators:

Expectation of Answer Changes:

This should not change results, because we don't yet generate efflux in any tests.

Checklist:

• I have updated the in-code documentation .AND. (the technical note .OR. the wiki) accordingly.
• I have read the CONTRIBUTING document.
• FATES PASS/FAIL regression tests were run

Test Results:

TBD

CTSM (or) E3SM (specify which) test hash-tag:

CTSM (or) E3SM (specify which) baseline hash-tag:

FATES baseline hash-tag:

Test Output:

[rgknox]

Including update to the pft index swapper tool.

[rgknox]

tested against baseline (temporary modification to ctsm5.1.dev056 that removes mosart tests from 1x1_brazil) :

fates-sci.1.47.1_api.17.0.0-ctsm5.1.dev056-RsFatesFix

Test results:
/glade/scratch/rgknox/tests_1010-122445ch

Expected DIFF against the base in: ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCru.cheyenne_intel.clm-FatesPRT2