RUU, Custom RUU, and APK

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RUU stands for ROM Update Utility. This is a utility that is run via a .exe file that is used to flash a stock ROM, stock radio, stock splash screen, stock recovery, and stock firmware of a device. The utility performs a cleaning of the NAND memory of the device before flashing the included stock software. So a RUU is often suggested as a way fix common problems and to unroot a device. The utility also runs a set of checks on a the
a device before flashing such as CID (Carrier Identification), battery level check, and firmware version check.

A custom RUU is does the same as a RUU but it has been modified to not run the CID check and sometimes other security checks. You can flash custom ROMs, different radio versions, splash screens, and firmwares. You can even use a custom RUU to flash each of these individually

A .apk file, or Application Package File, is the type of file used to distribute and install Android applications files in the Android OS. These files are in zip file format and contain all needed files, scripts, resources, and etc. that the application needs to function.