You use a XML layer file (layer.xml) as part of the installation system for your module. The contents of the layer.xml will be automatically included in the system filesystem when your module is installed.
When you use a module project template, a layer.xml file is automatically created for you. When you use a module file template to create a new action or to have the IDE recognize a new file type, the IDE automatically registers the new items in the layer.xml. You can use the System Filesystem Browser to tweak the layer.xml file, or you can do so manually using code completion in the Source Editor.