Though I have designed MineOS scripts to be as novice-friendly as possible, some features' usage is less clear without reading the code. This is a list of the most common features and issues of MineOS scripts.
The web interface is the preferred way to manage your Minecraft servers. Through the web-interface, you have the most synthesized and user-friendly output about the state of your servers as well as your versions, both MineOS and jarfiles. It is preferred to use the web-ui to perform any actions regarding your server unless you intend to have it automated (e.g., cronjob or shell scripts).
The shell scripts are located in /usr/games/minecraft and can be executed like ./mineos_console.py <options>. Console scripts are useful anytime a feature will be run as a timed event or with some addons not yet built into the web-ui. Click for a full listing of mineos_console.py commands and syntax.
./mineos_console.py should always be run as user mc, under all circumstances. Even when it is unavoidable that the script is called by root, ensure that mc is called with 'su' (substitute user), as for crontabs. If any files are modified or created as root, further attempts to access them via the web-ui will fail, as 'mc' will not have sufficient permissions. If, for example, the server is started as root, attempts to stop the server will be greeted with an error or blank page, upon failing to write to the lock files.
The core mineos_script is called 'mineos_console.py'. When performing actions from the shell or by crontab, you can follow the list of commands in the 0.5.0 Scripts page.
cd /usr/games/minecraft ./mineos_console.py -s servername command
cd /usr/games/minecraft ./update.sh
update.sh will download the most recent stable branch of MineOS scripts at http://minecraft.codeemo.com/crux/rsync/stable. Typically this route is only useful when you have somehow botched something and lost usability of the web-ui; the web-ui is the preferred way to update MineOS.
Addons are standalone shell scripts that will install an application entirely. To ensure you have all available add-on installation scripts, use 'Update MineOS' in the web-ui.
See the Add-ons page for a complete listing.