Hello,
The JS Package Generator currently only excludes the Plugin Codes inside the js/plugins.js File. We will release the possibilities of deleting the Plugin Codes from inside the js/functions.js in the Future Updates. Additionally, if you would like to do this manually, you can delete the Codes by following these instructions:
To delete, for example, the Flex Slider Plugin, find and the delete the loadFlexSlider: function() Function Block.
Delete all instances of the Function Calls: SEMICOLON.widget.loadFlexSlider(); .
This will definitely work fine. Hope this Helps!
Let us know if we can help you with anything else or if you find any further issues.