Protect iTop setup
The setup wizard used during first install could be disabled to reduce attack surface. Two files are particularly concerned :
setup/index.php : of course
setup/phpinfo.php : gives lots of informations about the system (note that risk is mitigated by adding authentication since iTop 2.5.2, 2.6.1 and 2.7.0)
You shouldn't remove the whole setup/ directory as it contains files that are necessary for iTop.
Instead you could block web access using a file appropriate to the web server you're using. Such files are already present in the data/ directory, for example :
* Apache httpd : https://github.com/Combodo/iTop/blob/develop/data/.htaccess
* Microsoft IIS : https://github.com/Combodo/iTop/blob/develop/data/web.config
To ease iTop update, you might want to automate the procedure. See Automated installation.