most basic way of getting a hex file onto a board: 

avrdude -p m328p -c avrisp2 -P usb -U flash:w:<path>:i

most basic way of getting hex file from a board:

avrdude -p m32u4 -c avrisp2 -P usb -U flash:r:<path>:i

most basic way of reading fuses (this will show all fuses, though it looks like it's only reading the low fuse):

avrdude -p m32u4 -c avrisp2 -P usb -U lfuse:r:-:i -v

most basic way of writing fuses:

avrdude -p m32u4 -c avrisp2 -P usb -U lfuse:w:<lfuse>:m -U hfuse:w:<hfuse>:m -U efuse:w:<efuse>:m

32U4 known working fuses for using with Arduino: 0XFF 0XD8 0XCB