e2e: cover setup selective merge and idempotence

[codeaholicguy]

Current coverage

The only setup E2E runs against an empty isolated HOME and asserts missing Codex/Pi directory guidance.

What is missing

• setup --agent codex, --agent pi, comma-separated selection, and invalid selection
• Actual generated hooks/configuration
• Merge with existing user Codex and Pi settings
• Repeated-run idempotence and duplicate prevention
• Partial integration failure and tmux guidance
• Permission/conflict handling

Risk ranking

High, rank 7: setup writes user-level integration files, but E2E currently verifies no write path.

Recommended E2E tests

• Preseed Codex and Pi user config, run selective and repeated setup, and assert user keys survive with no duplicated hooks.

Acceptance criteria

• The checklist tests are merged under e2e/.
• Tests isolate HOME and assert exact before/after configuration.
• Codex-only, Pi-only, combined, invalid, and repeated setup are covered.

Related audit findings

A8: runtime support depends on platform tools and needs explicit readiness behavior. D6: capability metadata can drive accurate setup/status reporting.