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I don't care if this is done in the bios or a kernel module or software. Is there any way at all to do make the 'fn' key act as 'control' and the 'control' key act as 'fn' in linux running on a macbook pro?

PS. You can do this with software in OSX with the application KeyRemap4MacBook.

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I think this is hardwired in the keyboard. Not sure, though. –  maxelost Jan 24 '11 at 16:36
    
Pretty sure it's not hardwired, because OSX can receive 'standalone' fn key events, meaning no other keys are being simultaneously pressed. –  coderrr Feb 12 '11 at 22:23
    
I can't give you an exact answer, but look at how the authors of these keyboard layout files change the mappings of keys. I find that changing regular keys is rather trivial. With a bit of patience and by studying the other examples (where those files should be installed) you might be able to figure out how to remap the control and fn keys. colemak.com –  Ярослав Рахматуллин Sep 18 '13 at 7:38
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I personally haven't needed to do this, but this link shows that you should be able to modify the kernal keymapping upon booting to make this switch.

This link also states that XFree86 will try and load the kernal mapping at its load time so it shouldn't need to be changes just for X if you do the above first.

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