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If you are just replacing the hardware, you can just relink the Oracle Homes and Applications executables via adadmin, run autoconfig and you are good to go. There is no need to clone unless you want to change the SID or domain.
R11i / R12 : How to relink an E-Business Suite Installation of Release 11i and Release 12.x ? (Doc ID 356878.1)
check the listener, it should be down while configuring apps.
Thanks for the suggestion this is what i was looking for , i did the re link and the application started after some hiccups for HTTPS server as i am using oracle linux 7 previous version of app server was 5.5 ,followed this document http://mohamedbh.blogspot.sg/2015/01/r12-apache-service-issue-error-while.html
to overcome the http issue ,
lets see ,user is testing now ,hopefully it wont crash(last one crash because we just restored the backup but didnt re-link)