Where does the core inject all this javascript?

I'm trying to find out where the core automatically injects javascript in my page. I use Bootstrap theme, and I came to the conclusion that I have 2 jquery scripts, and a load of other scripts as well that are included automatically on my page. Google proposes to change the place on the page, in order to speed the rendering, so I would like to know where the core does that, and perhaps alter the behaviour.