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Windows 2000 keeps an alternate copy of the registry hives (.ALT) and attempts to switch to it when corruption is detected. Windows XP and Windows Server 2003 do not maintain a System.alt hive because NTLDR on those versions of Windows can process the System.log file to bring up to date a System hive that has become inconsistent during a shutdown or crash. In addition, the %SystemRoot%\Repair folder contains a copy of the system's registry hives that were created after installation and the first successful startup of Windows.
In Windows, use of the registry for storing program data is a matter of developer's discretion. Microsoft provides programming interfaces for storing data in XML files (via MSXML) or database files (via SQL Server Compact) which developers can use instead. Developers are also free to use non-Microsoft alternatives or develop their own proprietary data stores.