Custom Dojo Loader Plugin for loading ESRI modules that you want the build system to ignore.

EsriLoader.js

define(function () {
    // summary:
    //      A dojo loader plugin for loading esri modules so that 
    //      they get ignored by the build system.
    return {
        load: function (id, require, callback) {
            // id: String
            //      esri module id
            // require: Function
            //      AMD require; usually a context-sensitive require bound to the module making the plugin request
            // callback: Function
            //      Callback function which will be called, when the loading finished.
            require([id], function (mod) {
                callback(mod);
            });
        }
    };
});

You use it like this:

define(['yourPackage/EsriLoader!esri/map'], function(Map) {/*...*/});

so this is working? the build doesn't try to flatten the dependency?

I thought the usage was more like

define(['app/EsriLoader!esri/map'], function(Map) { /* ... */ });

Since it's using require to load the module, it seems like it'd need to be a slash, not a period.

You're right @brianarn. I need to get out of the "." habit from the old dojo.require days.

Yes, @steveoh, it's working. I've successfully tested the build. The build system does not flatten nested requires. @brianarn was the one that enlightened me.