For those who need a very small software footprint I have updated the old Nios I UART drivers to the NIOSII. They are non blocking. They will work if even if you run them starting with alt_main. If start your code with main you will want make copy the alt_sys_int.c file from your syslib and place it in your software project directory. Then edit it to remove the calls to the HAL uart drivers and any other HAL based drivers that you do not want. Caution - this copy in your software project will not get updated when your hardware project changes.
Just places the simple_uart.c and simple_uart.h in your software project, and refresh the project. Cal