On June 20, 2013, a system update brought the introduction of the and Saved Data Backup feature. When apps inside folders receive StreetPass or SpotPass notifications, a notification icon will appear on top of the folder Only the first character of the title will be displayed on the folder's icon. A title for the folder is automatically created in order of creation (from '1' to '60'), but the name can also be edited by the user. Applications can be dragged on top of a folder in order to move it, and from then on, more apps can be added to the folder using the same procedure, up to 60 apps per folder. On April 25, 2012, a system update brought the introduction of a folder system. Using the HOME button, users can suspend the current software that is running and bring up the HOME Menu, allowing the user to launch certain multitasking applications, such as the Internet Browser and Miiverse. It is also possible to change the screen's brightness while in the menu. On the upper screen, a special 3D animated logo is displayed for each individual app, as well as system information such as wireless signal strength, date and time, and battery life, while on the bottom screen, application icons are displayed. The menu can display up to 300 application tiles for applications on the SD card, and up to 40 for DSiWare titles. The number of icons per column can also be changed, from 1 icon up to 6. Application icons are set in a grid navigable with the touchscreen or D-pad and may be re-arranged via drag-and-drop. It is used to launch software stored on Nintendo DS and Nintendo 3DS Game Cards, applications installed on an SD card, and DSiWare titles installed in the system's internal memory.

The HOME MENU is a graphical shell similar to the Nintendo DSi Menu and Wii U Menu for Nintendo 3DS and Nintendo 2DS systems. The NATIVE_FIRM is different on the New Nintendo 3DS. Finally, AGB_FIRM is the Game Boy Advance's native firmware and it is used to run Game Boy Advance Virtual Console games. TWL_FIRM is the Nintendo DSi's native firmware and it is used for Nintendo DS/DSi backward compatibility. SAFE_MODE_FIRM is used for safe mode applications, such as System Settings and System Updater. NATIVE_FIRM is the native firmware running the kernel for Nintendo 3DS software (including the Home Menu). The Nintendo 3DS firmware can run in four different modes.

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