updates from Erik's comments

python/ctsm/site_and_regional/neon_site.py

@@ -52,9 +52,6 @@ def build_base_case(
 
         return case_path
 
-    # def get_batch_query(self, case):
-    #    return super().get_batch_query(case)
-
     # pylint: disable=too-many-statements
     def run_case(
         self,
@@ -105,10 +102,6 @@ def run_case(
             base_case_root, run_type, prism, run_length, user_version, tower_type, user_mods_dirs
         )
 
-    def set_ref_case(self, case):
-        super().set_ref_case(case)
-        return True  ### Check if super returns false, if this will still return True?
-
     def modify_user_nl(self, case_root, run_type, rundir, site_lines=None):
         # TODO: include neon-specific user namelist lines, using this as just an example currently
         if site_lines is None:

python/ctsm/site_and_regional/run_neon.py

@@ -174,6 +174,8 @@ def main(description):
     """
     cesmroot = path_to_ctsm_root()
     # Get the list of supported neon sites from usermods
+    # The [!Fd]* portion means that we won't retrieve cases that start with:
+    # F (FATES) or d (default). We should be aware of adding cases that start with these.
     valid_neon_sites = glob.glob(
         os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!Fd]*")
     )

python/ctsm/site_and_regional/tower_site.py

@@ -243,6 +243,7 @@ def set_ref_case(self, case):
         return True
 
     # pylint: disable=too-many-statements
+    # TODO: This code should be broken up into smaller pieces
     def run_case(
         self,
         base_case_root,