Personally, I'd abstract it out in to its own plugin. You don't have to share it if you don't want to (though it might be nice), since the CLIs can install locally. That way you can version track it nicely, and it will continue to play nice with the CLI.
Essentially you can duplicate the plugin's code tree, adjust the code as necessary (copy your changed files), and then alter the plugin.xml as needed. After that, uninstall the original barcode plugin and install yours (cordova plugin add path/to/plugin). Then if you need to make additional changes, do them in the plugin and then rm/add it again.