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WinAPE v2.0 Alpha 18
You cannot pass a game name to the emu through CLI, but the emu will autolaunch the game set in its ini file.
Run the exe manually and goto Settings->General, check "Disable Automatic Update"
On the Display tab, check "Hide Control Panel", "Hide Menus" and "No Right-Click Menu". "Linear Palette" will slightly darken image if you enable it.
On the Sound tab, check "44 kHz" and "16 bit".
On the Input tab, set your controls and hit OK.
Press F10 to turn on fullscreen then ALT+F4 to exit and save your settings.
Roms should be zipped