Referencing js files with roots 7.0.2

Although I am not new to roots as such, clearly things are a bit different since the last couple of updates and I want to take full advantage of the benefits roots brings.

What I am struggling to understand is the purpose of the gruntfile. My understanding is that anything referenced within the 'jsFileList' array will be validated and minified, is this correct? So by adding a file to this array, all that means is that that file will be validated and minified, correct?

Where, then, do you reference a javascript file - for example I am trying to use a jquery plugin - scrollReveal.js. Do I just reference in the head or is there another place to put it? The reason I am so confused is if I view the source, and search for 'bootstrap' for example, nothing is being referenced, meaning there must be something else going on.

Any help would be much appreciated.

Thanks

Craig