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auto-merge.yml interpolated ${{ github.event.workflow_run.head_branch }} straight into a run script that holds a contents:write token. A fork pull request controls that branch name, so it could run commands with write access (CodeQL actions/code-injection/critical). It now arrives as an environment variable.
ci.yml, code-quality.yml and deploy.yml get permissions: contents: read; none of them writes through GITHUB_TOKEN.