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The XML-RPC subsystem gives external systems the opportunity to communicate with the site through the XML-RPC protocol. Pointing an XML-RPC client at http://sitename/xmlrpc.php allows this communication to take place. For more information, see the online handbook entry for XML-RPC API.
The user module allows users to register, log in, and log out. Users benefit from being able to sign on because this associates content they create with their account and allows various permissions to be set for their roles.
The system module provides system-wide defaults to running jobs at particular times, storing (caching) web pages to improve efficiency, and performing other essential tasks. The module also keeps track of various preferences you give for how you want your system to behave.