The OS uses a table of settings, usually called setup, that is accessible with the syscalls GetSetupSetting and SetSetupSetting. It is possible that all the OS settings are stored in this table. The setup appears to the user as if it was stored in the MCS item SETUP, but it is not actually stored in the MCS - it is stored in RS memory, address ranges 0xFD80xxxx (on the "fx-CG10/20 Manager" emulator, it starts at 0xFD801060).
The values are OS-wide, which means that changing a setting in one application changes it for all applications. The exception is eActivity files and strips: files and strips inside those files each have a separate setup.
On the Prizm, the setup table has space for 200 entries.
A limited setup editor can be accessed from most built-in OS applications by pressing SET UP (Shift+Menu). From the TestMode, one can access a setup editor that lists almost all options. There are some options, such as the keyboard input mode (Shift, Alpha, Clip, etc.) which are present in the setup but don't show in any of the editors, not even the TestMode one.
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