Hi!

I want to run a pd patch on the RPI3 that uses the makey makey keystrokes as input. I just want to know if the patch run with the -nogui flag still get the keystrokes.

I also want to know how you have managed to run a pd patch on boot on Raspbian Jessie, I have read a lot of forums, but none have worked for me.

Thank you very much.

The patch should work without the gui, I don't see a reason why it wouldn't. But you have to try for yourself.
For the Pi with Raspbian Jessie you need to edit crontab. In Pi's terminal type:
crontab -e

Then, at the end of the file type the following:
@reboot sleep 20 ; sh /home/pi/path/to/scripts/script_to_launch_pd.sh
where "script_to_launch_pd.sh" is a bash script that launches Pd.

The script should be something like:

#!/bin/bash
/usr/bin/pd -nogui -open /path/to/your/patch.pd &

This should launch Pd on boot of the Pi. If you want to go on and edit the patch while Pd is fired on boot, type this:
sudo killall pd
and Pd will be killed so you can work on your project further.