fix: Retain Quarantine After Failed Environment Setup

[danny-avila]

Summary

• Clear the startup mutation marker only after setup exits successfully without a timeout.
• Retain quarantine on nonzero exits, timeouts, and exceptions; explain inspection and reset in the startup error and docs.
• Extend real native CLI coverage to verify failure retains the marker and a second startup cannot rerun setup.

Fixes #211.

Verification

• Package TypeScript build passed.
• Four opt-in real native SRT CLI tests passed locally: success, nonzero failure, timeout, and maintenance reset.
• Failure cases verify durable quarantine and restart rejection before repeated mutation; success verifies marker removal before registration.
• Existing operators must inspect failed setup before using the existing quarantine reset command. No server configuration changes.

[danny-avila]

@codex review

Please review the current PR head a8498d8. Confirm that this exact commit is the reviewed commit and ignore findings that apply only to earlier heads.

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-14T23:52:33.734804Z	88c776b	Manual request

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[danny-avila]

@codex review

Please review the current PR head f8ba126. Confirm that this exact commit is the reviewed commit and ignore findings that apply only to earlier heads. This head also runs the real native setup lifecycle regressions in macOS CI.

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: f8ba12629a

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[danny-avila]

@codex review

Please review the current PR head 88c776b. Confirm that this exact commit is the reviewed commit and ignore findings that apply only to earlier heads.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. 🎉

Reviewed commit: 88c776b2b5

ℹ️ About Codex in GitHub

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