Configuring a firewall for example, or using a version control system as git or subversion, ssh, PECL and PEAR if you are using PHP, building and using a chroot, dealing with compilation of a program: it's not true that if not compiled is not stable, imagemagick for example is available by apt but you must compile it from source to tune or just to match your server and application features, same story for nginx, apache, gearman, php and mysql. But there is a lot more to take in consideration, it depends on your role (configuring everything or just the httpd server?) and in the application you want to develop.
cereal
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cereal