A module in an EAR may have alt-dd specified. From the application.xsd:

The moduleType defines a single Java EE module and contains a
connector, ejb, java, or web element, which indicates the
module type and contains a path to the module file, and an
optional alt-dd element, which specifies an optional URI to
the post-assembly version of the deployment descriptor.

Support for alt-dd in deployers project has been done in JBDEPLOY-27