Improvements and fix for fates-auto-params

[samsrabin]

As discussed at ESCOMP#2336.

Improvements:

• run_sys_tests now checks modules needed for modify_fates_paramfile for all testmods that call that in shell_commands. Required bringing in ctsm5.1.dev166.
• Reduces code duplication in FATES testmods' shell_commands by having them use new script cime_config/testdefs/testmods_dirs/clm/_scripts/get_fates_shell_commands_vars.sh.

Fix: Create directory for file output by ncgen, if needed. That's the mkdir -p call in get_fates_shell_commands_vars.sh.

Testing
./run_sys_tests -f testlist_fates --skip-compare --skip-generate now works on both Derecho and Izumi, where testlist_fates contains:

SMS_D_Ld3.f10_f10_mg37.I2000Clm50FatesRs.MACHINE_intel.clm-Fates
SMS_D_Ld3.f10_f10_mg37.I2000Clm50FatesRs.MACHINE_intel.clm-FatesColdSeedDisp
SMS_D_Ld3.f10_f10_mg37.I2000Clm50FatesRs.MACHINE_intel.clm-FatesColdTwoStream
SMS_D_Ld3.f10_f10_mg37.I2000Clm50FatesRs.MACHINE_intel.clm-FatesColdTwoStreamNoCompFixedBioGeo