Could be useful a default InitialContextFactory in modeshape so a client can call it through jndi. Here an example:

Hashtable<String, Object> jndiContext = new Hashtable<String, Object>();
jndiContext.put("java.naming.factory.initial","org.modeshape.common.naming.DummyInitialContextFactory");
jndiContext.put("java.naming.provider.url","localhost");
InitialContext initialContext = new InitialContext(jndiContext);

It is enough to add two classes in modeshape-common project.