Unsubscribe and ignore automatically every repository of your organisation.

gh-unsubscribe.sh

#!/usr/bin/env bash

# GH_TOKEN=
# GITHUB_TOKEN=$GH_TOKEN
# ORGANIZATION=
# LOG_FILE=

exec 3>&1 1>>${LOG_FILE} 2>&1

now=$(date)
echo ">>>> Script started at: $now"
echo ""

gh auth login --with-token <<< $GH_TOKEN

subscribed=($(gh api -H "Accept: application/vnd.github.json" -H "X-GitHub-Api-Version: 2022-11-28" /user/subscriptions --jq '.[].full_name') )
echo ">> Unsubscribe automatically subscribed repositories from $ORGANIZATION"
echo "$subscribed"
for it in "${subscribed[@]}"
do
    if [[ $it == *"$ORGANIZATION"* ]]; then
        gh api \
        --method PUT \
        -H "Accept: application/vnd.github+json" \
        -H "X-GitHub-Api-Version: 2022-11-28" \
        "/repos/${it}/subscription" \
        -F subscribed=false \
        -F ignored=true | jq .
    fi
done
echo ""

echo ">> Cleaning notifications"
gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" /notifications --jq '.[].repository.full_name'
notified=($(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" /notifications --jq '.[].repository.full_name'))
echo "$notified"
for it in "${notified[@]}"
do
    # Mark them as read. Missing steps :
    # unsubscribe (/notifications/beta/unsubscribe) + done (/notifications/beta/archive)
    if [[ $it == *"$ORGANIZATION"* ]]; then
        gh api \
        --method PUT \
        -H "Accept: application/vnd.github+json" \
        -H "X-GitHub-Api-Version: 2022-11-28" \
        "/repos/${it}/notifications"
    fi
done
echo ""

now=$(date)
echo ">>>> Script ended at: $now"

FIXME : Unfortunately, there's no way to unsubscribe notifications or mark them as done. For now the beta apis exist but are not accessible via gh. There might a chance that you will be spammed with "read" notifications if the script does not unsubscribe repositories between an automatic subscribe and operated changes on those repositories.

Another option that might help to avoid automatic subscription at all is the "Automatically watch repositories > When you're given push access to a repository, automatically receive notifications for it." notifications setting from your profile. However, as a global setting it would prevent you to automatically watch repositories that do not belong to a specific organisation.