remove HAL device drivers (preprocessor options)

One way to disable the UART driver is to add a file named 'altera_avalon_uart.h' to your system library project. This file should contain the following:

#define ALTERA_AVALON_UART_INSTANCE(name, device)   # define ALTERA_AVALON_UART_INIT(name, device)  

This will stop the HAL installing it's driver, and allow you to provide your own instead. If you want to initialise your driver before main(), you can use these macros - as described in the Nios II Software Developers' Handbook.