Let's say you have this folder structure:

projects/
	dojo/
		buildscripts/
	foo-project/
		src/
			foo/
				Bar.js

...where projects/foo-project/src/foo/Bar.js contains:

    dojo.provide("foo.Bar");
    foo.Bar=function(){ ... }

...in your custom profile.js script, you need to specify the module prefixes, something to this effect:

var dependencies = [
	"dojo.io.IO",
	"dojo.event.*",
	"dojo.io.BrowserIO",
	"dojo.xml.Parse",
	"dojo.webui.widgets.*",
	"dojo.webui.DomWidget",
	"dojo.animation.*",
	"foo.Bar"
];

dependencies.prefixes = [
	// this HAS to be relative to DOJO_HOME/ folder
	['foo', '../foo-project/src/foo']
];

load("getDependencyList.js");