How to know what files to include in Nios II main file?

Yes after experimentation I found what files are needed, depends on what we are doing.

alt_stdio for stdin and stdout

system.h always needed as it has constants needed for HAL functions

io.h if we are using the iord and iowr functions

peripheral headers e.g alt_timer_regs.h if we are using the timer as it contains timer specific HAL functions that are easier to use then IORD and IOWR

if we use usleep then we need unistd.h

if we are using interrupts that need to be registerd then we must include alt_irq.h

then if we are using HAL types like alt_uint16 then we need alt_types.h too

yes it keeps going