t1043: Align verify ShellCheck with CI and fix Phase 7b reconciliation

[marcusquinn]

Summary

• Fix 1: Post-merge ShellCheck verification used bare shellcheck (all severities) while CI uses -S error. This caused false verify_failed on pre-existing SC2016/SC1091 info-level violations. Now uses -S warning -x — catches real issues, skips info/style noise, follows source directives.
• Fix 2: Phase 7b reconciliation tried to transition verify_failed → complete when TODO.md showed [x], but the state machine doesn't allow that. Now excludes verify_failed from Gap 2 reconciliation — it's a meaningful state, not a stale inconsistency.

Impact

• All 8 verify_failed tasks failed due to ShellCheck severity mismatch (false positives)
• Phase 7b was logging "Failed to transition" errors every pulse cycle for these tasks
• After deploy, re-running verify on these tasks should pass with the relaxed severity

Files Changed

• .agents/scripts/supervisor/deploy.sh — run_verify_checks() shellcheck case: add -S warning -x
• .agents/scripts/supervisor/todo-sync.sh — reconcile_db_todo() Gap 2: exclude verify_failed

Summary by CodeRabbit

Release Notes

• Chores
  • Updated task reconciliation logic to properly handle post-deployment verification state, preventing unnecessary task reprocessing.
  • Enhanced shell script validation settings to align verification severity levels and source directive handling between local and CI environments.

[gemini-code-assist]

Summary of Changes

Hello @marcusquinn, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses issues related to task verification and state reconciliation within the supervisor system. It resolves false verify_failed statuses by adjusting ShellCheck's severity threshold to match CI, and prevents continuous reconciliation errors by correctly classifying verify_failed as a terminal state, ensuring the system accurately reflects task completion and verification outcomes.

Highlights

• ShellCheck Verification Alignment: Aligned post-merge ShellCheck verification with CI by using -S warning -x flags, resolving false verify_failed tasks caused by pre-existing info-level violations (SC2016/SC1091).
• Phase 7b Reconciliation Fix: Excluded the verify_failed state from Phase 7b reconciliation, preventing "Failed to transition" errors when TODO.md marked tasks as complete, as verify_failed is now treated as a meaningful terminal state.

Changelog

• .agents/scripts/supervisor/deploy.sh
  • Updated the shellcheck command in run_verify_checks() to include -S warning -x flags.
  • Added comments explaining the new ShellCheck flags and their purpose.
• .agents/scripts/supervisor/todo-sync.sh
  • Modified the reconcile_db_todo() function to exclude verify_failed from the list of non-terminal states in the Gap 2 reconciliation query.
  • Updated comments to reflect verify_failed as a terminal state and explain its exclusion from reconciliation.

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[coderabbitai]

Walkthrough

Two supervisor automation shell scripts are refined for production quality: deploy.sh receives ShellCheck invocation flag adjustments (-S warning, -x) to align with CI severity expectations, while todo-sync.sh evolves its reconciliation logic by recognizing verify_failed as a terminal state, preventing unnecessary task reconciliation for already-deployed-but-post-check-failing items.

Changes

Cohort / File(s)	Summary
ShellCheck Invocation Hardening .agents/scripts/supervisor/deploy.sh	Added -S warning flag for CI severity alignment and -x flag to follow source directives, preventing SC1091 false positives from sourced files.
Terminal State Logic .agents/scripts/supervisor/todo-sync.sh	Added verify_failed to the terminal-state exclusion filter in TODO.md reconciliation logic; includes documentation explaining that verify_failed (PR merged+deployed but post-merge checks failed) is handled by re-verification, not reconciliation.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Possibly related PRs

• t311.3: Extract supervisor modules #1220: Modifies the terminal states set in todo-sync.sh reconciliation logic, directly related to the verify_failed state addition.
• fix: add ShellCheck enforcement to CI code-quality workflow (t135.6) #432: Adjusts ShellCheck invocation flags in supervisor deployment scripts; related to the -S warning and -x flag enhancements.

Poem

🔧 Shell scripts shine with flags refined,
Verify_failed finds its place in line,
CI severity and sources aligned,
Zero debt gleams—automation divine! ✨

🚥 Pre-merge checks | ✅ 4

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately summarizes both main changes: ShellCheck alignment with CI and Phase 7b reconciliation fix, directly matching the changeset.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Merge Conflict Detection	✅ Passed	✅ No merge conflicts detected when merging into main

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch hotfix/supervisor-verify-improvements

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[github-actions]

🔍 Code Quality Report

�[0;35m[MONITOR]�[0m Code Review Monitoring Report

�[0;34m[INFO]�[0m Latest Quality Status:
SonarCloud: 0 bugs, 0 vulnerabilities, 26 code smells

�[0;34m[INFO]�[0m Recent monitoring activity:
Fri Feb 13 19:07:50 UTC 2026: Code review monitoring started
Fri Feb 13 19:07:50 UTC 2026: SonarCloud - Bugs: 0, Vulnerabilities: 0, Code Smells: 26

📈 Current Quality Metrics

• BUGS: 0
• CODE SMELLS: 26
• VULNERABILITIES: 0

Generated on: Fri Feb 13 19:07:53 UTC 2026

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Generated by AI DevOps Framework Code Review Monitoring

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[gemini-code-assist]

Code Review

This pull request introduces two well-justified fixes to the supervisor scripts. The first change aligns the post-merge ShellCheck verification with CI by adjusting the severity level, which will reduce noise from stylistic issues and prevent false positives. The second change correctly updates the database reconciliation logic to treat verify_failed as a meaningful terminal state, preventing incorrect state transitions. Both changes are clear, well-commented, and improve the overall robustness and reliability of the system. The code quality is high and I have no further suggestions.