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.
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In Unix-like operating systems (including Linux) that follow the Filesystem Hierarchy Standard, system-wide configuration files (information similar to what would appear in HKEY_LOCAL_MACHINE on Windows) are traditionally stored in files in /etc/ and its subdirectories, or sometimes in /usr/local/etc. Per-user information (information that would be roughly equivalent to that in HKEY_CURRENT_USER) is stored in hidden directories and files (that start with a period/full stop) within the user's home directory. However XDG-compliant applications should refer to the environment variables defined in the Base Directory specification.
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The "HKLM\SYSTEM" key is normally only writable by users with administrative privileges on the local system. It contains information about the Windows system setup, data for the secure random number generator (RNG), the list of currently mounted devices containing a filesystem, several numbered "HKLM\SYSTEM\Control Sets" containing alternative configurations for system hardware drivers and services running on the local system (including the currently used one and a backup), a "HKLM\SYSTEM\Select" subkey containing the status of these Control Sets, and a "HKLM\SYSTEM\CurrentControlSet" which is dynamically linked at boot time to the Control Set which is currently used on the local system. Each configured Control Set contains:
Individual settings for users on a system are stored in a hive (disk file) per user. During user login, the system loads the user hive under the HKEY_USERS key and sets the HKCU (HKEY_CURRENT_USER) symbolic reference to point to the current user. This allows applications to store/retrieve settings for the current user implicitly under the HKCU key.