There is only one command, looks something like:
C:\Program Files\Arduino\hardware\tools\avr/bin/avrdude -CC:\Program Files\Arduino\hardware\tools\avr/etc/avrdude.conf -v -patmega328p -carduino -PCOM3 -b115200 -D -Uflash:w:C:\Users\RAEBEL~1\AppData\Local\Temp\build939b42114286ff6d2142eb1235a39421.tmp/Matrix_trial.ino.hex:i
It's only shown when verbose upload output is enabled.
(this was pulled from another post here, since I'm not home)
Notice how it gives you the full paths to avrdude, avrdude.conf, and so on.