My question is similar but slightly different.  I am running my own custom
Spring-like container with an embedded version of Tomcat 5.5.  I have my own
JNDI Context object configured in my application that I bind objects to. 
However all those objects in that Context are not available to my web
applications because Tomcat is using it's own Context:

Context ctx = new InitialContext();
DataSource myDS = (DataSource) ctx.lookup( "java:/myDataSource" );

javax.naming.NameNotFoundException: Name myDataSource is not bound in this
Context
        at org.apache.naming.NamingContext.lookup(NamingContext.java:769)
        at org.apache.naming.NamingContext.lookup(NamingContext.java:152)
        at org.apache.naming.SelectorContext.lookup(SelectorContext.java:136)
        at javax.naming.InitialContext.lookup(InitialContext.java:347)

I am starting up my application as per this article:
http://www.vsj.co.uk/articles/display.asp?id=319.  All the documentation
I've seen has been using the server.xml which is not available to me as I'm
using the Embedded tomcat.  If I can use server.xml with Embedded.java,
please let me know.

Thanks
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