core.js

(function(global) {
	var config = false,
		modules = [];

	// setup single public namespace
	var skel = global.skel = {
		init: function(c) {
			// put initial config in the public scope
			config = c;

			for(var i = 0; i < modules.length; i++) {
				modules[i].run(config);
			}
		},
		register: function(module) {
			if(!module.run) {
				throw new Error("Modules must provide at minimal a run() function");
			};

			modules.push(module);

			if(module.register) {
				modules.register(config);
			};
		}
	}	
})(this);

run.js

skel.init();

skelmodule.js

(function(skel) {
	skel.register({
		name: "skeleton",
		run: function(config) {
			// do some stuff
			var x = 1;
			return x;
		}
	});
})(skel);

In this situation, run.js would be the last in the build.xml concatanation and gets this started. Modules register themselves if they need to do anything at runtime. init() then runs each of the modules after initing itself.