Hi, in the IDE's preferences, you can enable Verbose for compiling and uploading. The orange log in the bottom section will show you the steps, and at some point it will show the .bin file in a temporary location. It will also show you the full avrdude command to upload the .bin file.
The IDE puts the Arduino/Industruino in bootloader mode by 'forcing reset using 1200bps open/close on port /dev/ttyACM0' (in my case)
This can be done in Linux command line:
stty -F /dev/ttyACM0 ispeed 1200 ospeed 1200
Then the Industruino backlight fades in/out, indicating the bootloader is active. I think it's similar on Mac but i don't know about Windows.
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