Why? It's not designed to work with CI, you'll probably have to mess about alot to get it working. See one of the many versions available for CI here https://github.com/vesparny/codeigniter-html5boilerplate-twitter-bootstrap.
Further more, I dont see any great advantage of having a bootstrap CI integration, if you do then go for it but I just use my own customised bootstrap and load it in as normal in template/view files. Works just fine and keeps all those UI/view bits and pieces separate for designers/Front-end coders who panic at the sight of php.
All this work trying to keep design, function and layout separate and people go to great effort to ruin it with something like this.