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Normally folder does not disapear.
You might have (misconfigured) cron jobs to clean-up or admins that don't want to have anything in the root's home.
Or just another user removing that directory.
Thansk for reply.
I understand that its not normal for folder to go missing all of a sudden and most likely its a case of user doing such changes but that is not the case with us. Recently found some worms doing wget to phishy link plus large number of $JBOSS_HOME/deploy/kisses.tar.gz. not sure where did it come from but i think missing Jboss folder might have something to do with it. I was trying to look into something on server machine itself which could point to what might have caused the trouble with jboss. No clue yet.