Hey Tomas,
You will need to use 2 JavaScript Extensions, one for the plugins and modules and the other for the do_plugins section.
First you need to copy all the plugins and modules and paste them into a javascript extension. Give this a title such as "Plugins and Modules." The Plugins and Modules start with /*****Plugins******/ and goes down to the line that says, /**DO NOT ALTER ANYTHING BELOW THIS LINE****/.
Then copy the do_plugins code and paste it in another JavaScript Extension. Make sure this extension is below the "Plugins and Modules" extension. The do_plugins code should start with s.usePlugins=true and go down to the the /*******Plugins*******/ line.
Where you are working with raw JavaScript make sure and test this in a dev environment (or using Web Companion) before pushing this live.
Hope this helps.