(From my email to grails dev mailing list...)
Hi Grails Devs,
For a project I am working on, I am using Grails 0.6-RC1, and
embedding components (jars, configs etc) from another pre-existing
project, unfortunately these components expects JNDI support from the
app server. I posted an email last week to Grails-User for help but
receives no advice, so I took the matter into my own hands 
I made the following modification to Grails to enable JNDI in run-app:
== mod to GRAILS_HOME/scripts/Init.groovy ==
Line 41: enableJndi = System.getProperty('enable.jndi') == "true" ?
true : false
== mod to GRAILS_HOME/scripts/RunApp.groovy ==
/* within the import section */
import org.mortbay.jetty.plus.naming.*
import javax.naming.*
...
/*
within task configureHttpServer section right after:
webContext = new WebAppContext("${basedir}/web-app", "/${grailsAppName}")
*/
if (enableJndi) {
def confClassList =
["org.mortbay.jetty.webapp.WebInfConfiguration",
"org.mortbay.jetty.plus.webapp.EnvConfiguration",
"org.mortbay.jetty.plus.webapp.Configuration",
"org.mortbay.jetty.webapp.JettyWebXmlConfiguration",
"org.mortbay.jetty.webapp.TagLibConfiguration"]
webContext.setConfigurationClasses((String[])confClassList )
}
== additons to GRAILS_HOME/lib ==
jetty-naming-6.1.4.jar
jetty-plus-6.1.4.jar
With the above modifications, when I do this from command line:
MyProjectRoot/ > grails -Denable.jndi=true run-app
the embedded jetty instance will have JNDI support built-in.
If you like this, I can send a patch...
Improvement
Resolved
Major
add JNDI support to grails run-app 
Attached patch file generated from Eclipse/subclipse.
However, since I am adding 2 additional jar files, patch file does not include them, and Ivy doesn't seem to be completely integrated into the env, so I am attaching the jar files explicitly.