Решение:
<script type="text/javascript" src='/js/1.js'></script>
<script type="text/javascript" src='/js/2.js'></script>
    <script type="text/javascript">
        $(function () {
            alert(pp.core.aa);
            alert(pp.debug.bb);
            alert(pp.core.aa);
        });
    </script>
1.js
var pp = pp || {};
pp.core = {
    aa: 12
};
2.js
var pp = pp || {};
pp.debug = {
    bb: 13
};
 пример с входными параметрами
 

<script type="text/javascript">
        var pp = pp || {}; 
        pp.options = {
            color: '#fff111',
            duration: 'fast',
            complete: null,
            setup: null
        };
        pp.init = function (options) {

 значения по умолчанию

       

    pp.options = $.extend(pp.options, options);
            alert(pp.options.color);
        }
        pp.core = {
            aa: 12
        };    
    </script> 
    <script type="text/javascript">
        var pp = pp || {}; 
        pp.debug = {          
            bb:13
        };
        </script>
    <script type="text/javascript">
        $(function () {
            pp.init({ color: '#222222'});
            alert(pp.core.aa);
            alert(pp.debug.bb);
            alert(pp.core.aa); 
        });
    </script>