"mvn --reactor" will search subdirectories for pom.xml files and dynamically build a reactor using them. You can also specify includes/excludes directory with -Dmaven.reactor.includes and -Dmaven.reactor.excludes.
It would be nice to be able to use this with the Maven Invoker... but look at DefaultInvocationRequest. It has a method called "activateReactor":
It would be helpful if it were implemented.