The MIUI flag configer is my first android app and was a solution to give the user the ability to configure the custom rom he is about to install.
As you can guess from the name it was designed for the MIUI rom but it works with Cyanogenmod or any other rom, too.
Einsteinno1 provided configuring his rom by adding flags into the file name of the installation package.
The flag configer is just an user interface for reading and changing these flags. Everything else is done by the installation script.
Nowadays this app is highly deprecated and not used anymore because it was replaced by tools of other great developers.
One example is the AROMA-Installer.