The code can be combined by writing your own Angular directives which generate HTML that has Bootstrap classes. I am working on a similar web application that combines Bootstrap with Angular. What I did there, was something like this:
app.directive('trackerMenu', function(){
    return {
        restrict: 'E',
        templateUrl: "partials/menu.html"
    };
});
And the content of menu.html is:
<nav class="navbar navbar-default navbar-fixed-top" role="navigation" ng-show="auth">
<div class="container-fluid">
    <div class="navbar-header">
        <a class="navbar-brand">Issue Tracker</a>
        <ul class="nav navbar-nav">
            <li class='toggleable'>
                <a ng-click="navigate('dashboard')"><i class="fa fa-home"></i>Dashboard</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('tasks')"><i class="fa fa-tasks"></i>Tasks</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('bugs')"><i class="fa fa-bug"></i>Bugs</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('statistics')"><i class="fa fa-bar-chart-o"></i>Statistics</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('team')"><i class="fa fa-users"></i>Team</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('profile')"><i class="fa fa-user"></i>Profile</a>
            </li>
            <li class='toggleable'>
                <a ng-click="navigate('settings')"><i class="fa fa-cog"></i>Settings</a>
            </li>
        </ul>
        <form class="navbar-form navbar-left" role="search">
            <div class="input-group">
                <input type="text" class="form-control" placeholder="Search">
                <span class="input-group-addon"><i class="fa fa-search"></i></span>
            </div>
        </form>
        <ul class="nav navbar-nav">
            <li>
                <a ng-click="logout()"><i class="fa fa-power-off"></i>Logout</a>
            </li>
        </ul>
    </div>
</div>
</nav>
And the directive is used like this:
<body ng-class="togglePadding()" ng-controller="RootCtrl">
    <tracker-menu></tracker-menu>
</body>
Basically, what my directive does is to inject a Bootstrap navbar into a page.