Make sure you are using Yeoman 1.0 and not an earlier version. It uses grunt-requirejs which has almond support. rjs was used in versions before 1.0.
See documentation at https://github.com/asciidisco/grunt-requirejs/blob/master/docs/almondIntegration.md. It appears that all you may need to do is add almond: true
to the options for requirejs in your Gruntfile (or not depending on what you want to do--again see the documentation).