As described in the Modules API, you can use an XML filesystem layer as part of the installation system for your module; the contents of the layer will be automatically included in the system filesystem only when your module is installed. The API Support includes support for creating and manipulating XML layers to make it easier for you.
To learn more about layers in general, check the following topics in the Open APIs:
Layers (general)
Layer XML syntax
Action installation
(The links above will only work if you have the module
Open APIs Documentation installed.)