After restarting the SCM-Manager, the plugins that we copy on to the disk/directory will get deleted by SCM restart as it extracts the WAR and overwrites anything on the target. Only the CORE plugins will be retained. The directory where the Instructions is pointing to will be overwritten each time the SCM restart.
The correct way is to
(1) Find out the correct directory where all other plugins are present but not the core plugins directory
(2) Copy the custom-links plugin
(3) Restart the scm-manager