Thanks for all the input.
@sonnyyu, that link was very helpful.
To be clear, I want to compile the sketch in the IDE, sftp the *.cpp.hex into linux side, connect USB-A to micro-usb, and tell avrdude to upload it to 32u4 via the micro-usb.
Can I run this from linux side, where is whatever port is assigned, i.e. /dev/ttyACM0 ?
1) Connect/disconnect serial@1200 to reset and start bootloader
2) avrdude -C/etc/avrdude.conf -v -patmega32u4 -cavr109 -P<port> -b57600 -D -Uflash:w:sketch.cpp.hex:i
I tried the above and it seemed to upload the sketch but the sketch failed to run. I also lost the usb connection to the microusb. I had to upload a sketch via the IDE wifi/ethernet to restore the yun’s micro-usb and normal functionality. I noticed the IDE uses a newer version of avrdude and config file. Copying over this config to the Yun also did not work. Avrdude errored out for syntax… perhaps incompatibility to the config file. Closer but not there yet.