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deployment issue

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Hi I have deployed a j2ee application on linux through

command interface using application server webphere 6.0

I have a sepearte java project in form of jar file that need

to be deployed on same linux system
facing problem becuase it is command base .no user interface

or no ide on that system otherwise windows no issue at all
1)Now if I keep java project in any folder on linux can i

use the jre inside websphere or should i use the sepearte

jre(jdk) installed in different folder

2)or should I deploy this jar file on websphere application

server.if yes how to do it.means in which folder I should

keep this jar file.
I wont prefer this option as this jar contains some jar file

which are also presnt in websphere lib and both may

contradict or corrupt the whole system

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