when u already create some custom made plugin, it surely show in setup and design area but when you open home page on spesific journal it would vanish.
on such term we need to update ojs 2 / register the new custom made plugin to ojs it self how to do it. Try running the upgrade script (php tools/upgrade.php upgrade) — after backing up your database, that is, just in case.
and here the step to install new plugin
Installation ------------ To install the plugin: - Unpack the plugin tar.gz file to your plugins/generic directory - From your application's installation directory, run the upgrade script: $ php tools/upgrade.php upgrade (NOTE: It is recommended to back up your database first.) - Enable the plugin by going to: Management > Website Settings > Plugins > Generic Plugins ...and selecting the Enable checkbox beside "Custom Block Manager Plugin"