The _include.ini files represent standard outputs by EddyPro and are meant to help minimize the amount of manual input needed to generate first stage ini files.
EddyPro_Common_FirstStage_include.ini should be used anytime EddyPro software is used for EC data processing, while other EddyPro_instrument_FirstStage_include.ini files are setup dependent.
These ini files can be incorporated into first stage ini files using #include filename