This is the system file you should include as a matter of last resort if you are developing for the ATMega1284P but your actual board is not listed in the sys folder. ie it is for a generic ATMega1284P board. This may also be because you have created your own ATMega1284P based board. Consequently the library assumes that all processor pins have header pins.
It will make sure that your compiler settings are appropriate: ie ATMega1284P