It means you would type "NoMariosSky.exe -resetPrefs" without quotes in the command line at NoMariosSky.exe's path. "NoMariosSky.exe" is the command and "-resetPrefs" is an argument that the command understands. Hope this also resets your controls.
OK so -resetPrefs worked as intended. It didn't reset the controls but I've set them to what I believe to be the default controls.