That's not enough. The "make" command will place the new fop2 web files in /var/www/html/fop2 , so when you browser FOP2 on your system you are using the OLD web files with the NEW server, and that won't work at all. You will need to copy files and subdirectories in /var/www/html/fop2 to your custom directory (you must update client files also).
Not only that, having a custom directory means that you also need to modify autoconfig-users.sh script and set the PLUGINDIR variable by hand to match. Otherwise plugins won't work either.
Best regards,
