Did the old alt_irq_register, alt_irq_enable\disable functions get taken out? I'm using quartus 12 and it seems like they only have some new IRQ related functions in alt_irq.h, what gives?
They should be present, the new interrupt API is the default though. If you take a look at the system.h file you should see a macro called something like "ENHANCED_INTERRUPT_API" set to 1 which causes the new API to be used. For more details I would take a look at this document: http://www.altera.com/literature/hb/nios2/n2sw_nii52006.pdf