If `#methods` traverse the super class, it includes the methods that
were does `undef` in the subclass.

Before patched:
```terminal
% bin/mruby -e 'p Module.instance_methods - Class.instance_methods'
[]
```

After patched:
```terminal
% bin/mruby -e 'p Module.instance_methods - Class.instance_methods'
[:append_features, :extend_object]
```