update clean option

tools/Readme.configure

@@ -46,11 +46,15 @@ optional arguments:
                         for each machine, use the utility manage_case in this
                         directory. The default is the first listing in MPILIBS
                         in config_machines.xml
+  --clean               Remove old Macros and env files before attempting to
+                        create new ones
+
+
 
 It will create a Macros file in make or cmake format along with the module support
 for the specified or default compiler.   It will also create two files
 .env_mach_specific.csh
 .env_mach_specific.sh
 
 Before you try to run make you should source the file above appropriate for your shell
-this will set the proper environment for supported systems which use modules.
+this will set the proper environment for supported systems which use modules.

tools/configure

@@ -67,7 +67,7 @@ def parse_command_line(args):
     parser.add_argument("--clean", action="store_true", 
                         help="Remove old Macros and env files before attempting to create new ones")
 
-
+    argcnt = len(args)
     args = parser.parse_args()
     CIME.utils.handle_standard_logging_options(args)
 
@@ -85,12 +85,6 @@ def parse_command_line(args):
 
     opts['machobj'] = machobj
 
-    if args.clean:
-        files = ["Macros.make", "Macros.cmake", "env_mach_specific.xml", ".env_mach_specific.sh", ".env_mach_specific.csh"]
-        for file_ in files:
-            if os.path.isfile(file_):
-                os.remove(file_)
-
     if args.macros_format is None:
         opts['macros_format'] = []
     else:
@@ -139,12 +133,25 @@ def parse_command_line(args):
         os.environ["DEBUG"] = "FALSE"
     opts['debug'] = debug
 
+
+    if args.clean:
+        files = ["Macros.make", "Macros.cmake", "env_mach_specific.xml", ".env_mach_specific.sh", 
+                 ".env_mach_specific.csh", "Depends.%s"%compiler, "Depends.%s"%args.machine,
+                  "Depends.%s.%s"%(args.machine,compiler)]
+        for file_ in files:
+            if os.path.isfile(file_):
+                logger.warn("Removing file %s"%file_)
+                os.remove(file_)
+        if argcnt == 2:
+            opts['clean_only'] = True
+
     return opts
 
 def _main():
     opts = parse_command_line(sys.argv)
-    configure(opts['machobj'], opts['output_dir'], opts['macros_format'],
-              opts['compiler'], opts['mpilib'], opts['debug'], opts['os'])
+    if "clean_only" not in opts or not opts["clean_only"]:
+        configure(opts['machobj'], opts['output_dir'], opts['macros_format'],
+                  opts['compiler'], opts['mpilib'], opts['debug'], opts['os'])
 
 if __name__ == "__main__":
     _main()