There is an SPI called ConfigurationProvider that allows you to implement a custom solution for providing the PrettyFaces configuration. PrettyFaces uses this SPI internally to provided different mechanisms for configuration like XML or annotations. But you can also use the SPI yourself to implement custom ways of building the configuration.
Just create an implementation of ConfigurationProvider
and then add a file called META-INF/services/com.ocpsoft.pretty.faces.spi.ConfigurationProvider
to your classpath and add the full class name of your implementation class there (see this example for such a file and the javadocs of ServiceLoader for a descriptions of this plugin mechanism).