Little issue

Why Yii puts two times same complete JS library under assets directory instead of one ?

The copy under assets is published from framework and is thus accessible to end users. Without this publishing process, you will need to manually maintain where to put those js files and their URLs.

Yeah, I know that. But why Yii put me same directory with same files twice, just under different names.

That's because you upgraded Yii. You can safely remove everything under assets so that only one copy will be there.