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JDK 1.5 to JDK 1.6

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I am migrating an application from WAS6.1 to WAS8, from java 1.5 to java 1.6.

Migration highlighted one behaviour change. 'Check the JAXB context factory initialization class'
Currently the application code on (java 1.5 run on WAS6.1) references external jaxb 2.x jars
On researching , what I understood is WAS8.0 comes bundled with its on version of JAXB.(rt.jar)
What is the right thing to do? Remove the reference to the external jars and use the jaxb jar that comes bundled with
WAS8.0 or leave the code as it is and compile and checkin the code.

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