We all like to think our website are secure until the inevitable happens you get hacked or your hosting provider gets hacked your sites down and you lose revenue. Securing your site with file permissions is usaully covered by you hosting provider but at responsive web design we also host some of our sites using linux machines so we need to go a little bit further when our own security is at risk.
Locking down our server is done by only allowing those who need access to files read and write permissions to alter them via FTP and ensuring none of the files or directories have the 777 file permissions on them.
Keeping Debian or fedora updated is often overlooked when web developers lurch into the VPS route so keep the system updated and constantly review your firewalls and antivirus to be sure your VPS is not hacked.
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Keeping any system epically your own vpn should be the highest proirity as most attacks exploit vulnerabilities in older versions that system fixes and bugs have not been applied.