app.js

window.app = angular.module('myApp', []);

articles.js

function ArticlesController($scope) {
  $scope.articles = {}
}

config.js

window.app.config(function($routeProvider) {
  $routeProvider
    .when('', {})
    .otherwise('', {});
})

index.html

<script src="jquery.min.js"></script>
<script src="angular.min.js"></script>

<script src="app.js"></script>
<script src="config"></script>

<script src="controllers/articles"></script>
<script src="init.js"></script>

init.js

window.bootstrap = function() {
    angular.bootstrap(document, ['myApp']);
}

window.init = function() {
    window.bootstrap();
}

$(document).ready(function() {
    window.init();
});

Another way to organize controllers:

controllers = {};
controllers.ArticleCtrl = function($scope) {[]};

window.app.controller(controllers);