It took me a while to find how to write the build script to omit duplicate dependencies included in the global but required by the page-specific scripts. For instance, we have a custom form handler called MyProject.form and is extended by page-specific classes. So, with the original build this class was included in the Global layer and the page-specific layer resulting in the MyProject.form class being in both .js files in the built page.

The answer is: layerDependencies in the build script.

dependencies = {
    resourceName: "MyProject",
    layers: [
    {
        name: "../../MyProject/Global.js",
        dependencies: ["MyProject", "MyProject.Global"]
    },
    {
        name: "../../MyProject/CategoryPage.js",
        dependencies: ["MyProject.CategoryPage"],
        layerDependencies: ["../../MyProject/Global.js"]
    }
    ]
};

So,  if a class in dojo.required (and therefore included) in Global.js it will be not be copied into CategoryPage.js if it is required there, also.