Move fix for transient non-crop to release-clm5.0 branch

[ekluzek]

Description of changes

Move changes from ctsm1.0.dev013 to release-clm5.0 branch. This is the fix for transient non-crop simulations.

Specific notes

Contributors other than yourself, if any: none

CTSM Issues Fixed (include github issue #): #538

Are answers expected to change (and if so in what way)? Yes (for non-crop clm45/clm50 transient cases)
Currently generic crop areas stay at 1850 levels. This fix allows them to change as they should.

Any User Interface Changes (namelist or namelist defaults changes)? Just for mksurfdata.pl

Testing performed, if any: None now (but was done on master) will be repeated before accepted.

NOTE: Be sure to check your Coding style against the standard:
https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines

[ekluzek]

Testing as expected:

================================================================================
These tests compare different to the baseline
================================================================================
ERP_D.f10_f10_musgs.IHistClm50Bgc.cheyenne_gnu.clm-decStart
ERP_D.f10_f10_musgs.IHistClm50Bgc.cheyenne_intel.clm-decStart
ERP_D_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay (missing baseline)
ERP_D_Ld5.f19_g17.IHistClm50Bgc.cheyenne_intel.clm-drydepnomegan
ERP_P36x2_D_Ld5.f10_f10_musgs.IHistClm45BgcCruGs.cheyenne_intel.clm-decStart
ERP_P36x2_Lm13.f10_f10_musgs.IHistClm50Bgc.cheyenne_gnu.clm-monthly
ERP_P36x2_Lm13.f10_f10_musgs.IHistClm50Bgc.cheyenne_intel.clm-monthly
ERS_D_Ld10.f10_f10_musgs.IHistClm50SpG.cheyenne_intel.clm-glcMEC_decrease
SMS_D_Ly2.1x1_brazil.IHistClm50BgcQianGs.cheyenne_intel.clm-ciso_bombspike1963
SMS_Ld5.f19_g17.IHistClm50Bgc.cheyenne_intel.clm-decStart
SMS_Ly1_Mmpi-serial.1x1_brazil.IHistClm50BgcQianGs.cheyenne_gnu.clm-output_bgc_highfreq
================================================================================
These tests failed
================================================================================
ERP_D_Ld10_P36x2.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_decStart		EXPECTED
ERS_D_Ln9_P480x3.f19_g16.I2000Clm50SpGs.cheyenne_intel.clm-waccmx_offline		EXPECTED
ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropGs.cheyenne_gnu.clm-monthly		EXPECTED
ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-monthly		EXPECTED

================================================================================
These tests compare different to the baseline
================================================================================
ERP_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-decStart
SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-decStart
SMS_Ld5_D_P48x1.f10_f10_musgs.IHistClm50Bgc.hobart_nag.clm-monthly
================================================================================
These tests failed
================================================================================
SMS.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop		EXPECTED
SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop		EXPECTED