Hi Micah,

If your module includes JSPs or .java files, it will need to be compiled before it can be deployed. I added a note to the page you linked to help clarify.

https://www.labkey.org/wiki/home/Documentation/page.view?name=customizingBuild

The build will also automatically do things like compress HTML and JS files, though this step is not required for a successful deployment.

Thanks,
Josh