That's a file from Nios classic days. It contains information about your system such as the address mapping for each peripheral connected to the Nios processor core.
The file you want to look for (Nios II) is now called "system.h" which lives in the system library in the following location /<Debug or Release>/system_description. It provides the same type of information that nios.h contained.
To become familiar with the new software flow I recommend taking the hardware design that you are using for the DE2 board, open then IDE and add a simple software project like "hello world", compile it then take a look at the resulting folder structure. I also recommend taking a look at this document:
http://www.altera.com/literature/an/an350.pdf (
http://www.altera.com/literature/an/an350.pdf)
That'll help explain what has changed between Nios classic and Nios II in terms of software development.