RequireJS modules loading out of order when loading one module into another

I have written a web application which uses requirejs for AMD:

require(dependencies, function(dependencies) { 
    (function($) {
        $.fn.plugin = function(options) { return this; };
    })(window.jQuery);
});

I then used almond and r.js to compile it into a single javascript file, using the build config:

({
    baseUrl: ".",
    paths: {
        'jquery' : 'vendor/jquery-1.9.1.min'
        'almond' : "../node_modules/almond/almond"
    },
    name : "almond",
    include : "main",
    out : "plugin.js",
    wrap : true
})

Next, I want to use this plugin in another app, also based on requirejs. Here I have:

require.config({ paths: { 'jquery': 'vendor/jquery-1.9.1.min' } });
require(['jquery','plugin'], function ($) {
    $('#plugin').plugin(options);
});

However, the code loads out of order:

1. Load jquery and plugin js files.
2. Execute $('#plugin').plugin(options).
3. Run (function($) { $.fn.plugin = function(options) { return this; }; })(window.jQuery);

Obviously, (2) is an error since (3) needs to be run first. The question is, why?

UPDATE 1

One proposed solution is to change the first block of code to:

define(dependencies, function(dependencies) { 
    (function($) {
        $.fn.plugin = function(options) { return this; };
    })(window.jQuery);
});

Once compiled, this becomes:

define("main", dependencies, function(dependencies) { 
    (function($) {
        $.fn.plugin = function(options) { return this; };
    })(window.jQuery);
});

Unfortunately, now the code inside this block is NEVER executed.