Keyboard Mapping
How to personalise keyboard's buttons
The mapping for Control, Option, and Command are according to the physical layout of the keys on an actual MacBook keyboard, not the labels on the keys. Control=Control, Windows=Option, and Alt=Command. If you want a more PC friendly keyboard layout, use Karabiner
(formerly KeyRemap4MacBook). You can find it here.
The function of Fn+F1..F12 and F1..F12 can be changed in SysPrefs->Keyboard.
Personally i only changed the right ctrl to be mapped to the right alt.
Troubleshooting
If you get issues with keyboard mapping and you decide to reset it:
sudo rm /Library/Preferences/com.apple.keyboardtype.plist
and then reboot. After reboot the Assistant asks to verify the layout, bingo !
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