1. Update stale peptiderepo/peptide-e2e ref to peptide-repo/peptide-e2e.
Reusable workflow uses: refs do not follow GitHub transfer redirects.
2. Fix permissions: contents: read → write so nested reusable ci.yml
(requires write for phpcbf auto-commit) can run without startup_failure.
Agent-Session: fix-e2e-ref-20260617