Fix commandline arg merging, small improvements

Commandline args should be merged with the submodule's config.
Compare config values to None instead of False, so empty lines and False
can be used as values.

lib/python/milc.py

@@ -180,7 +180,7 @@ class ConfigurationSection(Configuration):
         """Returns a config value, pulling from the `user` section as a fallback.
         This is called when the attribute is accessed either via the get method or through [ ] index.
         """
-        if key in self._config and self._config[key]:
+        if key in self._config and self._config.get(key) is not None:
             return self._config[key]
 
         elif key in self.parent.user:
@@ -523,7 +523,7 @@ class MILC(object):
                     exit(1)
 
                 # Merge this argument into self.config
-                if argument in self.default_arguments:
+                if argument in self.default_arguments[section]:
                     arg_value = getattr(self.args, argument)
                     if arg_value:
                         self.config[section][argument] = arg_value
@@ -531,7 +531,7 @@ class MILC(object):
                     if argument not in self.config[section]:
                         # Check if the argument exist for this section
                         arg = getattr(self.args, argument)
-                        if arg:
+                        if arg is not None:
                             self.config[section][argument] = arg
 
         self.release_lock()