It would be nice to set different templates in the options. I want to use the (http://orgachem.github.com/JsDoc2-Template-Bootstrap/) template.

jsdoc : {
            options: {
                template: 'bootstrap'
            },
            dist : {
                src: ['lib/app.js'],
                dest: 'doc'
            }
        }

Not sure if this would be the best way but the easiest way would be to put the template files in: {Project Folder}/node_modules/grunt-jsdoc/node_modules/jsdoc/templates/bootstrap