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17.2.1.2. Why do this programmatically and not just put this in a jndi.properties file?

The JBoss application server's internal naming environment is controlled by the conf/jndi.properties file, which should not be edited.

No other jndi.properties file should be deployed inside the application server because of the possibility of its being found on the classpath when it shouldn't and thus disrupting the internal operation of the server. For example, if an EJB deployment included a jndi.properties configured for HA-JNDI, when the server binds the EJB proxies into JNDI it will likely bind them into the replicated HA-JNDI tree and not into the local JNDI tree where they belong.