A few tweaks.

interpreter.py

@@ -1577,6 +1577,7 @@ class Interpreter():
                 raise InterpreterException('Argument "configuration" is not of type configuration_data')
 
             conffile = os.path.join(self.subdir, inputfile)
+            if conffile not in self.build_def_files:
                 self.build_def_files.append(conffile)
             os.makedirs(os.path.join(self.environment.build_dir, self.subdir), exist_ok=True)
             ifile_abs = os.path.join(self.environment.source_dir, self.subdir, inputfile)

modules/gnome.py

@@ -62,7 +62,7 @@ class GnomeModule:
         scan_command += ['--namespace='+ns, '--nsversion=' + nsversion, '--warn-all',
                          '--output', '@OUTPUT@']
 
-        extra_args = kwargs.get('extra_args', [])
+        extra_args = kwargs.pop('extra_args', [])
         if not isinstance(extra_args, list):
             extra_args = [extra_args]
         scan_command += extra_args