Hi Chris,
__mulsi3 is the standard GCC single-width integer multiply routine. It is called when the compiler knows that the Nios II processor lacks integer multiply instructions. It's a
great place to put your multiply custom instruction. BTW, if you do any 64-bit math, you might see calls to __muldi3.
alt_exceptions.S contains the multiply and divide emulation routines, among other things. You can ignore these as long as the software of your system has been generated for Cyclone. The emulation routines are called only when a Nios II processor that lacks a hardware multiply attempts to execute a multiply instruction.
Kerry