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In preparation for our next UPD delivery, I am trying to cleanup our development environment and remove several instances of IFS apps 10 from our middleware server. What is the best practice to remove an installation of apps 10 from the middleware server in order to free-up resources (ports, memory, disk space etc.)?

The safest way is to use Delete option within the installer.cmd. This should delete all  IFS Services, sub directories and free up all the ports. Once the Delete process finishes, you can manually delete the IFS Home folder for the instance in questionand reboot the server to confirm all the changes.