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fix(52): replace stale MCP issue refs and refresh Wave 2 execution#494

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codex/52-wave2-followthrough
May 28, 2026
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fix(52): replace stale MCP issue refs and refresh Wave 2 execution#494
ashleyshaw merged 1 commit into
developfrom
codex/52-wave2-followthrough

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@ashleyshaw ashleyshaw commented May 28, 2026

Summary

Closes #52 by replacing stale MCP issue tool references and completing the requested live backlog refresh + formal Wave 2 reprioritisation updates.

Changes

#52 MCP tool reference alignment

  • Updated stale issue creation/read references in active agent and prompt specs:
    • create_issue -> issue_write
    • get_issue -> issue_read
  • Files updated:
    • agents/mode-prd.agent.md
    • .github/prompts/create-github-issue-feature-from-specification.prompt.md
    • .github/prompts/create-github-issues-feature-from-implementation-plan.prompt.md
    • .github/prompts/create-github-issues-for-unmet-specification-requirements.prompt.md
    • .github/prompts/my-issues.prompt.md

Changelog + next actions plan (requested first)

  • Updated CHANGELOG.md (Unreleased) with:
    • merged #64 + PR #461 status
    • merged policy hardening PR #463
    • this #52 MCP reference alignment
    • Wave 2 reprioritisation completion note
  • Updated .github/projects/active/next-issues-execution-plan-2026-05-27.md with:
    • current merged baseline (#61, #64)
    • Wave 1 now focused on #52
    • formal Wave 2A/2B/2C batch structure for #464-#490

Wave 2 reprioritisation pass (live issue updates)

  • Posted scheduling/progress comments on #464-#490.
  • Set Wave 2A core runtime batch (#464, #465, #466, #467, #468, #469, #476, #480, #482) to status:ready.

Validation

  • npm run lint:md -- CHANGELOG.md .github/projects/active/next-issues-execution-plan-2026-05-27.md .github/prompts/create-github-issues-feature-from-implementation-plan.prompt.md .github/prompts/create-github-issues-for-unmet-specification-requirements.prompt.md .github/prompts/create-github-issue-feature-from-specification.prompt.md .github/prompts/my-issues.prompt.md agents/mode-prd.agent.md
  • npm run test:js (pre-commit hook)

Summary by CodeRabbit

  • Documentation

    • Updated project execution plan to v1.1.0 with refreshed roadmap content, explicit Wave 2 batch organization (core runtime, planning agents, scaffolds) for upcoming development cycles, and revised execution sequencing.
  • Chores

    • Updated internal GitHub issue management tool references across agent configurations and prompt specifications to align with current platform APIs.

Review Change Stack

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coderabbitai Bot commented May 28, 2026

📝 Walkthrough

Walkthrough

This PR updates the project execution plan to version 1.1.0 with revised Wave 2 batching structure, and systematically migrates deprecated MCP tool references (create_issue → issue_write, get_issue → issue_read) across prompt and agent configuration files. Changes are documented in CHANGELOG.md.

Changes

Issue #52 Maintenance & Execution Plan Update

Layer / File(s) Summary
Execution Plan Update (2026-05-28)
.github/projects/active/next-issues-execution-plan-2026-05-27.md
Document version bumped from v1.0.3 to v1.1.0. Wave 1 ordering adjusted to prioritize #52 execution. Wave 2 expanded into three sub-batches (2A: core runtime burn-down, 2B: mode/planning agent, 2C: scaffolds/completion) with specific issue lists and execution dependencies. Proposed next action updated to continue #52 merge and open Wave 2A branch.
MCP Tool Reference Migration
.github/prompts/create-github-issue-feature-from-specification.prompt.md, .github/prompts/create-github-issues-feature-from-implementation-plan.prompt.md, .github/prompts/create-github-issues-for-unmet-specification-requirements.prompt.md, .github/prompts/my-issues.prompt.md, agents/mode-prd.agent.md
Replaced deprecated MCP tool references: create_issueissue_write in spec-from-feature, implementation-plan, and unmet-requirements prompts and mode-prd agent; replaced get_issueissue_read in my-issues prompt. Tool declarations and process instructions updated consistently across all files.
Changelog Documentation
CHANGELOG.md
Unreleased section expanded with entries documenting execution plan Wave 2 reprioritization with explicit burn-down batches for spec-only agent tasks (#464#490), and a Changed subsection documenting the MCP tool reference migration (create_issue → issue_write, get_issue → issue_read) for issue #52 alignment.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~8 minutes

Suggested labels

status:needs-review, type:bug, documentation, lang:md, priority:normal, meta:needs-changelog

🚥 Pre-merge checks | ✅ 5
✅ Passed checks (5 passed)
Check name Status Explanation
Title check ✅ Passed The title clearly summarizes the main change: replacing deprecated MCP tool references and refreshing Wave 2 execution planning, directly related to issue #52.
Description check ✅ Passed The description covers the main changes, includes a summary section, lists all modified files, provides changelog updates, and mentions validation steps performed.
Linked Issues check ✅ Passed The PR addresses all acceptance criteria from issue #52: replaced create_issue with issue_write, scanned for and replaced get_issue with issue_read, updated relevant files and documentation, and prepared changelog entries.
Out of Scope Changes check ✅ Passed All changes are scoped to issue #52 requirements and the Wave 2 execution plan refresh mentioned in the PR objectives. No unrelated modifications detected.
Docstring Coverage ✅ Passed No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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  • Commit unit tests in branch codex/52-wave2-followthrough

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@github-actions github-actions Bot added area:documentation Docs & guides lang:md Markdown content/docs status:needs-review Awaiting code review priority:normal Default priority type:chore Chore / small hygiene change type:bug Bug or defect meta:needs-changelog Requires a changelog entry before merge and removed type:chore Chore / small hygiene change labels May 28, 2026
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💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: c71ea31836

ℹ️ About Codex in GitHub

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Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

Comment on lines +9 to 11
"issue_write",
"search_issues",
"update_issue",
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P2 Badge Replace the remaining issue update tool

This prompt still allow-lists update_issue even though the change migrates issue creation to the consolidated MCP tool. I checked the current GitHub MCP issue tool list, where updates are handled by issue_write with method: 'update', and update_issue is no longer listed; in hosts that validate prompt frontmatter tool names exactly, the update-existing path can fail to load or become unavailable. The same stale allow-list entry appears in the other two issue-creation prompts.

Useful? React with 👍 / 👎.

Comment on lines +7 to 8
"issue_read",
"get_issue_comments",
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P2 Badge Replace the stale issue comments tool

This swaps get_issue to issue_read but leaves get_issue_comments in the prompt allow-list. The current GitHub MCP issue tools consolidate comment reads into issue_read with the get_comments method, so environments that exact-check prompt tool names can reject this prompt or leave the comment-count workflow without the declared read tool.

Useful? React with 👍 / 👎.

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Actionable comments posted: 2

🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In @.github/projects/active/next-issues-execution-plan-2026-05-27.md:
- Line 15: Add a single top-level H1 above the existing "## Next Issues
Execution Plan (2026-05-28)" heading so the file contains one H1 and subsequent
headings are sequential; specifically insert a "# Next Issues Execution Plan
(2026-05-28)" (or a brief equivalent H1 title) immediately before the current
"## Next Issues Execution Plan (2026-05-28)" line to satisfy the "*.md: Use one
H1 per file and keep heading levels sequential" guideline.

In `@agents/mode-prd.agent.md`:
- Around line 14-16: Add the new tool names "issue_write" and "issue_read" to
the validator allowlist by updating the validTools array in
scripts/validation/validate-agents.js so the agent config entries
("issue_write", "update_issue", "issue_read") are recognized; locate the
validTools symbol in that file and append these two strings to the list
(preserving formatting and any existing sorting conventions) so validation no
longer flags them as Unknown tool.
🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

  • Push a commit to this branch (recommended)
  • Create a new PR with the fixes

ℹ️ Review info
⚙️ Run configuration

Configuration used: Path: .coderabbit.yml

Review profile: CHILL

Plan: Pro

Run ID: 12809a52-d541-48f6-b25c-21136adbb058

📥 Commits

Reviewing files that changed from the base of the PR and between 2cca963 and c71ea31.

📒 Files selected for processing (7)
  • .github/projects/active/next-issues-execution-plan-2026-05-27.md
  • .github/prompts/create-github-issue-feature-from-specification.prompt.md
  • .github/prompts/create-github-issues-feature-from-implementation-plan.prompt.md
  • .github/prompts/create-github-issues-for-unmet-specification-requirements.prompt.md
  • .github/prompts/my-issues.prompt.md
  • CHANGELOG.md
  • agents/mode-prd.agent.md

---

## Next Issues Execution Plan (2026-05-27)
## Next Issues Execution Plan (2026-05-28)
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⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Add a single H1 before this section to keep heading levels sequential.

This starts at ## without a preceding #, which breaks the required heading structure for Markdown docs.

As per coding guidelines, "**/*.md: Use one H1 per file and keep heading levels sequential".

🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In @.github/projects/active/next-issues-execution-plan-2026-05-27.md at line 15,
Add a single top-level H1 above the existing "## Next Issues Execution Plan
(2026-05-28)" heading so the file contains one H1 and subsequent headings are
sequential; specifically insert a "# Next Issues Execution Plan (2026-05-28)"
(or a brief equivalent H1 title) immediately before the current "## Next Issues
Execution Plan (2026-05-28)" line to satisfy the "*.md: Use one H1 per file and
keep heading levels sequential" guideline.

Comment thread agents/mode-prd.agent.md
Comment on lines +14 to +16
"issue_write",
"update_issue",
"get_issue",
"issue_read",
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Update the agent-tools validator allowlist for issue_write/issue_read.

These new tool names are not in scripts/validation/validate-agents.js (validTools), so this config can be flagged as Unknown tool during validation.

Suggested fix
--- a/scripts/validation/validate-agents.js
+++ b/scripts/validation/validate-agents.js
@@
   const validTools = [
@@
     "todo",
     "todowrite",
+    "issue_write",
+    "issue_read",
   ];
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@agents/mode-prd.agent.md` around lines 14 - 16, Add the new tool names
"issue_write" and "issue_read" to the validator allowlist by updating the
validTools array in scripts/validation/validate-agents.js so the agent config
entries ("issue_write", "update_issue", "issue_read") are recognized; locate the
validTools symbol in that file and append these two strings to the list
(preserving formatting and any existing sorting conventions) so validation no
longer flags them as Unknown tool.

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🔍 Reviewer Summary for PR #494

CI Status:success
Files changed: 7

Recommendations

  • Ready to proceed pending human review

@ashleyshaw ashleyshaw merged commit 5f11844 into develop May 28, 2026
18 checks passed
@ashleyshaw ashleyshaw deleted the codex/52-wave2-followthrough branch May 28, 2026 06:43
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Update references from 'create_issue' to 'issue_write' and scan for outdated MCP tools

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