So it can be done, it just--required a lot of steps and me making a mapping spreadsheet of all the containers. But! Automations and scripts run in the homeassistant container, while when you ssh, you're going into the ssh addon container which should have been obvious and really was once I finished mapping all the containers.

Goal: I need /usr/local/bin in the ssh container so I can run scripts over ssh and access my function library script easily without ./path/to/script.

Summary: ssh into HAOS from the homeassistant container with an HAOS root user (port 22222), run docker exec to get into the ssh addon container, then make your symlinks for /usr/local/bin.

(Note: this is ridiculously complicated and I know there has to be a better way. But this works so I win.)

1. Get access to HAOS itself as root: https://developers.home-assistant.io/docs/operating-system/debugging. Verify you can login successfully.
2. In homeassistant container:

• a. create an .ssh folder (/config/.ssh)
• b. add the authorized_keys file you made for step one.
• c. add the public and private keys you made for step one (should be in the ssh addon container).
• d. set permissions;

chmod 600 /config/.ssh/authorized_keys
chmod 600 /config/.ssh/PRIVATE_KEY
chmod 644 /config/.ssh/PUBLIC_KEY
chmod 700 /config/.ssh

• e. In /config/shell_scripts.yaml or wherever you put your shell scripts, add the script you want to use to update /usr/local/bin: UPDATE_BIN_SCRIPT: /config/shell_scripts/UPDATE_BIN_SCRIPT
• f. Restart HA.
• g. Check it in Developer Tools->Services

I have no idea how consistent the ssh addon container name is usually but it's different on all three of my installs, so insert your container name for SSH_ADDON_CONTAINER_NAME

Steps: login to HAOS, go into the SSH Container, and do the update. This is horribly messy but hey, it works.

UPDATE_BIN_SCRIPT

#!/bin/bash

# OPTIONAL: Update some of the very outdated alpine packages in both homeassistant and the ssh addon (figlet makes cool ascii art of my server
# name).   You'll need to run it twice; once for the homeassistant container, then again in the ssh container.  Assuming you want to update packages,
# anyway
# update homeassistant container packages
apk add coreutils figlet iproute2 iw jq ncurses procps-ng sed util-linux wireless-tools

# ssh into HAOS and access docker container
ssh -i /config/.ssh/PRIVATE_KEY -p 22222 root@HA_IP_ADDRESS << EOF
	docker exec SSH_ADDON_CONTAINER_NAME \
	bash -c \
       'apk add coreutils figlet iproute2 iw jq ncurses procps-ng sed util-linux wireless-tools; \
	if [ ! -h /usr/local/bin/SCRIPT1 ]; then echo "SCRIPT1 does not exist"; \
	ln -s /homeassistant/shell_scripts/SCRIPT1 /usr/local/bin/SCRIPT1; echo "Link created"; \
	else echo "Link exists";fi; \
	if [ ! -h /usr/local/bin/SCRIPT2 ]; then echo "SCRIPT2 does not exist"; \
	ln -s /homeassistant/shell_scripts/SCRIPT2 /usr/local/bin/SCRIPT2; echo "Link created"; \
	else echo "Link exists";fi'
EOF

echo "Done"

I am going to feel really stupid when I find out there's a much easier way.