At the moment, modules are read from the layers configured on the source server (including base layer of course) and from the overlays if there are any.

There is another place to store modules in the server and that is the add-ons directory with the structure like:

<wildfly home>/modules/system/add-ons/<add-on name>/<module path>/<slot>/...

The class JBossServer.Modules needs to be enhanced to cope with those modules too.