Nios II Hardware Abstraction Layer (HAL) is a well defined software layer that forms a clear distinction between application and device-level software. The HAL also provides services such as file descriptors, I/O control, and buffering, which are required by the ANSI C library functions, so that your HAL driver does not need to provide these functions.

Articles:
LoadingCodeSections How to create custom sections and load them.
IRQCode  How the IRQ code works for the Nios II processor

Literature from Altera:
The Hardware Abstraction Layer Chapter in the Nios II Software Developer's Handbook
HAL API Reference Quick reference for HAL API functions 
Guidelines for Developing a Nios II HAL Device Driver Application Note

Nios II Hardware Abstraction Layer