Hi Bryan8,
to use the agent on ARM Linux boards (like Raspberry PI) you need to compile everything by yourself.
We currently package it only for Windows, Mac and Linux on 64bit Intel processors.
You can find the instructions to compile it here: GitHub - arduino/arduino-create-agent: The Arduino Create Agent
About the java IDE, it looks like your SD card is either full or broken, because the archive extracts and executes correctly on out test RPi . You probably also need to follow the guide about "adding udev rules" if the upload is not executing correctly (problems touching the port etc)