If you take a look at the documentation, you'll see that you have the option of including all of the js, or only the scripts you want using #= require
in your js/coffee files.
https://github.com/thomas-mcdonald/bootstrap-sass#javascripts
Same applies to stylesheets, you can use @import
to only include the files you want. You can look at the files architecture here:
https://github.com/thomas-mcdonald/bootstrap-sass/tree/master/vendor/assets/stylesheets
The gem is actually an engine, it basically just adds assets, the same way the jquery-rails gem adds jquery and you can use it as if you had a jquery.js file in your vendor/assets/javascripts
folder.