Many programming languages offer built-in runtime library functions or classes that wrap the underlying Windows APIs and thereby enable programs to store settings in the registry (e.g. Microsoft.Win32.Registry in VB.NET and C#, or TRegistry in Delphi and Free Pascal). COM-enabled applications like Visual Basic 6 can use the WSH WScript.Shell object. Another way is to use the Windows Resource Kit Tool, Reg.exe by executing it from code,[24] although this is considered poor programming practice.

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The key located by HKLM is actually not stored on disk, but maintained in memory by the system kernel in order to map all the other subkeys. Applications cannot create any additional subkeys. On Windows NT, this key contains four subkeys, "SAM", "SECURITY", "SYSTEM", and "SOFTWARE", that are loaded at boot time within their respective files located in the %SystemRoot%\System32\config folder. A fifth subkey, "HARDWARE", is volatile and is created dynamically, and as such is not stored in a file (it exposes a view of all the currently detected Plug-and-Play devices). On Windows Vista and above, a sixth and seventh subkey, "COMPONENTS" and "BCD", are mapped in memory by the kernel on-demand and loaded from %SystemRoot%\system32\config\COMPONENTS or from boot configuration data, \boot\BCD on the system partition.

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The registry contains important configuration information for the operating system, for installed applications as well as individual settings for each user and application. A careless change to the operating system configuration in the registry could cause irreversible damage, so it is usually only installer programs which perform changes to the registry database during installation/configuration and removal. If a user wants to edit the registry manually, Microsoft recommends that a backup of the registry be performed before the change.[17] When a program is removed from control panel, it is not completely removed and the user must manually check inside directories such as program files. After this, the user needs to manually remove any reference to the uninstalled program in the registry. This is usually done by using RegEdit.exe.[18] Editing the registry is sometimes necessary when working around Windows-specific issues e.g. problems when logging onto a domain can be resolved by editing the registry.[19]

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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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