diff --git a/driver_cpl/cime_config/config_component.xml b/driver_cpl/cime_config/config_component.xml
index cf4881ddda8..c1b10351181 100644
--- a/driver_cpl/cime_config/config_component.xml
+++ b/driver_cpl/cime_config/config_component.xml
@@ -1766,14 +1766,6 @@
     <desc>Machine name</desc>
   </entry>
 
-  <entry id="MACHINES_FILE">
-    <type>char</type>
-    <default_value></default_value>
-    <group>case_def</group>
-    <file>env_case.xml</file>
-    <desc>full pathname of file specifying supported machines location</desc>
-  </entry>
-
   <entry id="MACHDIR">
     <type>char</type>
     <default_value></default_value>
diff --git a/utils/python/CIME/XML/machines.py b/utils/python/CIME/XML/machines.py
index 5c861ca1311..8b83c9d6f61 100644
--- a/utils/python/CIME/XML/machines.py
+++ b/utils/python/CIME/XML/machines.py
@@ -27,9 +27,9 @@ def __init__(self, infile=None, files=None, machine=None):
         if infile is None:
             if files is None:
                 files = Files()
-            infile = files.get_value("MACHINES_SPEC_FILE")
+            infile = files.get_value("MACHINES_SPEC_FILE", resolved=False)
             self.machines_dir = os.path.dirname(infile)
-
+            infile = files.get_resolved_value(infile)
         GenericXML.__init__(self, infile)
 
         # Append the contents of $HOME/.cime/config_machines.xml if it exists
@@ -340,7 +340,7 @@ def get_full_mpirun(self, check_members, case, job):
         batch_system = self.get_value("BATCH_SYSTEM")
         if batch_system == "cobalt":
             mpi_arg_string += " : "
-        
+
         return "%s %s %s" % (executable if executable is not None else "", mpi_arg_string, default_run_suffix)
 
     def print_values(self):
diff --git a/utils/python/CIME/case.py b/utils/python/CIME/case.py
index 0ed270cd38d..fa73b36e342 100644
--- a/utils/python/CIME/case.py
+++ b/utils/python/CIME/case.py
@@ -91,7 +91,6 @@ def __init__(self, case_root=None, read_only=True):
         self._pesfile = None
         self._gridfile = None
         self._components = []
-        self._component_config_files = []
         self._component_classes = []
 
     # Define __enter__ and __exit__ so that we can use this as a context manager
@@ -399,12 +398,14 @@ def _get_component_config_data(self):
             comp_class = self._component_classes[i]
             comp_name  = self._components[i-1]
             node_name = 'CONFIG_' + comp_class + '_FILE'
-            comp_config_file = files.get_value(node_name, {"component":comp_name}, resolved=True)
+            # Add the group and elements for the config_files.xml
+            comp_config_file = files.get_value(node_name, {"component":comp_name}, resolved=False)
+            self.set_value(node_name, comp_config_file)
+            comp_config_file = self.get_resolved_value(comp_config_file)
             expect(comp_config_file is not None,"No config file for component %s"%comp_name)
             compobj = Component(comp_config_file)
             for env_file in self._env_entryid_files:
                 env_file.add_elements_by_group(compobj, attributes=attlist)
-            self._component_config_files.append((node_name,comp_config_file))
 
         # Add the group and elements for the config_files.xml
         for env_file in self._env_entryid_files:
@@ -474,10 +475,6 @@ def configure(self, compset_name, grid_name, machine_name=None,
 
         self.get_compset_var_settings()
 
-        # Add the group and elements for the config_files.xml
-        for config_file in self._component_config_files:
-            self.set_value(config_file[0],config_file[1])
-
         #--------------------------------------------
         # machine
         #--------------------------------------------
@@ -829,13 +826,17 @@ def create_clone(self, newcase, keepexe=False, mach_dir=None, project=None):
         # create clone from self to case
         clone_cimeroot = self.get_value("CIMEROOT")
         if newcase_cimeroot != clone_cimeroot:
+            case_branch = get_current_branch(clone_cimeroot)
+            clone_branch =  get_current_branch(newcase_cimeroot)
             logger.warning(" case  CIMEROOT is %s " %newcase_cimeroot)
             logger.warning(" clone CIMEROOT is %s " %clone_cimeroot)
-            logger.warning(" It is NOT recommended to clone cases from different versions of CIMEROOT")
+            logger.warning(" It is NOT recommended to clone cases from different versions of CIME.")
+
 
         # *** create case object as deepcopy of clone object ***
         srcroot = os.path.join(newcase_cimeroot,"..")
         newcase = self.copy(newcasename, newcaseroot, newsrcroot=srcroot)
+        newcase.set_value("CIMEROOT", newcase_cimeroot)
 
         # determine if will use clone executable or not
         if keepexe: