externals prevent creation of run directory for NEON cases.

[wwieder]

Brief summary of bug

Exernals update in dev172 created an issue with the run_dir not existing, #2437 (comment).

This prevents users from running postAD cases, after AD spinup. Presumably the same would be true of transient cases using the flag --run-from-postad, although I haven't tested this.

General bug information

CTSM version you are using: ctsm5.1.dev175

Does this bug cause significantly incorrect results in the model's science? No, but it limits utility of run_neon features

Configurations affected: postAD (and presumably transient cases using the option of --run-from-postad

Important details of your setup / configuration so we can reproduce the bug:

after running in AD mode the following command fails (with the error below)

./run_neon --neon-sites DEJU --run-type postad --experiment dev175 --output-root /glade/derecho/scratch/wwieder/neon_AK --overwrite

Important output or errors that show the problem

WARNING: No .input_data_list files found in dir 'Buildconf'
Time required to building the base case: 426.88800072669983 s.
using this version: latest
---- cloning the base case in /glade/derecho/scratch/wwieder/neon_AK/DEJU.postad
Traceback (most recent call last):
  File "./run_neon", line 48, in <module>
    main(__doc__)
  File "/glade/u/home/wwieder/CTSM/tools/site_and_regional/../../python/ctsm/site_and_regional/run_neon.py", line 241, in main
    experiment,
  File "/glade/u/home/wwieder/CTSM/tools/site_and_regional/../../python/ctsm/site_and_regional/neon_site.py", line 103, in run_case
    base_case_root, run_type, prism, run_length, user_version, tower_type, user_mods_dirs
  File "/glade/u/home/wwieder/CTSM/tools/site_and_regional/../../python/ctsm/site_and_regional/tower_site.py", line 395, in run_case
    self.set_ref_case(case)
  File "/glade/u/home/wwieder/CTSM/tools/site_and_regional/../../python/ctsm/site_and_regional/tower_site.py", line 230, in set_ref_case
    symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile)))
  File "/glade/u/home/wwieder/CTSM/cime/CIME/utils.py", line 1473, in symlink_force
    raise e
  File "/glade/u/home/wwieder/CTSM/cime/CIME/utils.py", line 1467, in symlink_force
    os.symlink(target, link_name)
FileNotFoundError: [Errno 2] No such file or directory: '/glade/derecho/scratch/wwieder/neon_AK/DEJU.ad/run/DEJU.ad.clm2.r.1018-01-01-00000.nc' -> '/glade/derecho/scratch/wwieder/neon_AK/DEJU.postad/run/DEJU.ad.clm2.r.1018-01-01-00000.nc'

The AD restart file exists, but it cannot be copied into the postAD/run directory, which doesn't exist.