This is the system file you should include as a matter of last resort if you are developing for the ATMega2561 but your actual board is not listed in the sys folder. ie it is for a generic ATMega2561 board. This may also be because you have created your own ATMega2561 based board. Consequently the library assumes that all processor pins have header pins.
It will make sure that your compiler settings are appropriate: ie ATMega2561