Is it safe to edit the configuration files from the shell or will this break InterWorx-CP?
Yes, it is safe to edit all of your configuration files from the shell without harming the control panel. InterWorx was designed that way. It parses the existing config files for settings to allow maximum customization. This does not preclude some of your changes from possibly being overridden in an update. The most common settings edited are those for Apache. To preclude them from being overwritten it is best to use a .htaccess file for single domains or additional apache cofiguration files placed in /etc/httpd/conf.d/. AllowOverride is set to All by default for just this reason. php.ini should be safe to edit. It is always best to keep local copies of the originals and your changes just in case you need to do a quick fix after an update.