Add close-issue safe output for automated issue cleanup

[Copilot]

Implementation Complete: close-issue Safe Output Type

Changes Made

• Create CloseIssuesConfig struct in pkg/workflow/compiler.go
• Create close_issue.go with parsing and job building logic (following close_discussion.go pattern)
• Create close_issue.cjs JavaScript implementation (following close_discussion.cjs pattern)
• Create close_issue.test.cjs comprehensive test suite ✅ NEW
• Update safe_outputs.go to include CloseIssues in:
  • HasSafeOutputsEnabled() function ✓
  • Safe output prompt generation ✓
  • MCP server tools enablement ✓
• Add schema definition to pkg/parser/schemas/main_workflow_schema.json
• Embed the JavaScript file in pkg/workflow/scripts.go
• Add getter function in pkg/workflow/scripts.go (getCloseIssueScript())
• Update semantic-function-refactor.md to use close-issue instead of update-issue
• Add close_issue tool to safe_outputs_tools.json
• Update compiler_jobs.go to build close_issue job
• Update test expectations in safe_outputs_tools_test.go
• Run tests and compile workflow to verify ✓

Test Coverage for close_issue.cjs

✅ 10 comprehensive test cases:

1. Handle empty agent output
2. Handle missing agent output
3. Close issue with comment in triggering context
4. Close specific issue when target is "*"
5. Filter by required title prefix
6. Filter by required labels
7. Skip already closed issues
8. Work in staged mode
9. Handle multiple issues in batch
10. Skip when not in issue context and target is triggering

Test Results

✓ All JavaScript tests pass (10/10 close_issue tests)
✓ All unit tests pass
✓ Linter passes
✓ Workflow compiles successfully (267.0 KB)

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[q] Close existing [refactor] issues before creating new one</issue_title>
<issue_description># Q Workflow Optimization Report

Context

This fix addresses issue #4543, where the semantic-function-refactor workflow was creating duplicate issues with the [refactor] title prefix. Currently, there are 7 open issues with this prefix, all created by this workflow.

Issue Evidence:

• Issue [refactor] 🔧 Semantic Function Clustering Analysis: Code Organization Refactoring Opportunities #4543 (this issue)
• Issue 📊 Daily Code Metrics Report - 2025-11-22 #4542: "[refactor] Refactor Redundant Network Allow-List Validation Logic"
• Issue Potential fix for code scanning alert no. 36: Incorrect conversion between integer types #4541: "[refactor] Consolidate Duplicated MCP Tool Rendering Across Engines"
• Issue [tidy] Fix code formatting: remove trailing whitespace #4540: "[refactor] Extract GitHub Copilot MCP Server Configuration to Shared File"
• Issue No test failures found - all tests passing #4539: "[refactor] Extract Duplicated MCP Server Configuration Rendering"
• Issue Fix test expectations for network hook script format #4538: "[refactor] Extract Tavily MCP Configuration to Shared File"
• Issue Fix ASCII art alignment by preserving per-line leading spaces #4537: "[refactor] Extract Shared Playwright Configuration into Reusable File"

Changes Made

Modified Workflow: semantic-function-refactor.md

1. Added Safe Output Capabilities

safe-outputs:
  update-issue:
    status:           # Allow closing issues
    target: "*"       # Allow targeting any issue (not just triggering)
    max: 10           # Allow closing up to 10 issues
  add-comment:
    max: 10           # Allow commenting on up to 10 issues
  create-issue:       # Existing create-issue config
    title-prefix: "[refactor] "
    labels: [refactoring, code-quality, automated-analysis]
    max: 1

2. Enhanced GitHub Tools

tools:
  github:
    toolsets: [default, issues]  # Added 'issues' toolset for issue operations

3. Updated Mission Instructions

Added explicit instructions to close existing [refactor] issues BEFORE performing analysis:

## Mission

**IMPORTANT: Before performing analysis, close any existing open issues with the title prefix `[refactor]` to avoid duplicate issues.**

Analyze all Go source files (`.go` files, excluding test files) in the repository to:
1. **First, close existing open issues** with the `[refactor]` prefix
2. Collect all function names per file
...

4. Added New Task Step

Inserted a new critical first step:

### 1. Close Existing Refactor Issues

**CRITICAL FIRST STEP**: Before performing any analysis, close existing open issues with the `[refactor]` prefix to prevent duplicate issues.

Use the GitHub API to:
1. Search for open issues with title containing `[refactor]`
2. Close each found issue with a comment explaining a new analysis is being performed
3. Use the `github-search_issues` and `github-issue_read` tools to find and close these issues

Example workflow:
1. Search: github-search_issues with query "is:issue is:open [refactor] in:title repo:${{ github.repository }}"
2. For each found issue:
   - Add comment: "Closing this issue as a new semantic function refactoring analysis is being performed."
   - Close the issue using update_issue tool

**Do not proceed with analysis until all existing `[refactor]` issues are closed.**

5. Updated Permissions

permissions:
  contents: read
  issues: read
  pull-requests: read
  actions: read       # Added for safe outputs

Note: Removed issues: write permission as the workflow uses strict: true mode. Write operations are handled safely through the safe-outputs system.

Expected Improvements

Immediate Impact

• Eliminates duplicate issues: Each workflow run will now close existing [refactor] issues before creating a new one
• Cleaner issue tracking: Only one active refactoring analysis issue at a time
• Better workflow hygiene: Prevents accumulation of stale refactoring recommendations

Behavior Change

Before:

• Workflow creates a new [refactor] issue each run
• Multiple duplicate issues accumulate over time
• 7 open issues with same purpose currently exist

After:

• Workflow searches for existing [refactor] issues
• Closes all found issues with explanatory comment
• Creates one new issue with fresh analysis
• Result: Always exactly 1 active [refactor] issue

Validation

✅ Workflow compiled successfully:

✓ .github/workflows/semantic-function-refactor.md (284.9 KB)
✓ Compiled 1 workflow(s): 0 error(s), 0 warning(s)

Schema Validation

• ✅ Safe outputs configuration validated
• ✅ Permissions validated in strict mode
• ✅ Tool configuration validated
• ✅ YAML frontmatter syntax validated

Testing Recommendations

1. Test the workflow manually using workflow_dispatch trigger
2. Verify it closes existing issues before creating new one
3. Check the comment text on closed issues is clear and informative
4. Confirm only one new issue is created after closing duplicates

Implementation Notes

• The workflow uses `sa...

• Fixes [q] Close existing [refactor] issues before creating new one #4552

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Pull request overview

This PR adds a new close-issue safe output type to enable automated cleanup of duplicate issues. The implementation follows the established close-discussion pattern and includes Go backend code, JavaScript execution script, JSON schema validation, and a practical example in the semantic-function-refactor workflow.

Key changes:

• Implements close-issue safe output with filtering by title prefix, labels, and target
• Adds security features (required title prefix prevents closing wrong issues)
• Supports batch operations (configurable max 1-100 issues)
• Includes cross-repo support via target-repo field

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pkg/workflow/close_issue.go	Core Go implementation with config parser and job builder
pkg/workflow/js/close_issue.cjs	JavaScript script for GitHub API operations (has critical bug)
pkg/workflow/safe_outputs.go	Integration points for safe output system
pkg/workflow/compiler.go	Type definition for CloseIssuesConfig struct
pkg/workflow/compiler_jobs.go	Job builder integration
pkg/workflow/scripts.go	Script embedding and bundling setup
pkg/parser/schemas/main_workflow_schema.json	JSON schema validation rules
pkg/workflow/js/safe_outputs_tools.json	MCP tool definition for AI agents
pkg/workflow/safe_outputs_tools_test.go	Test expectations update
.github/workflows/semantic-function-refactor.md	Example workflow using close-issue
.github/workflows/semantic-function-refactor.lock.yml	Compiled workflow output

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[pelikhan]

@copilot lint and fix JavaScript tests

[Copilot]

@copilot lint and fix JavaScript tests

Added comprehensive test suite for close_issue.cjs with 10 test cases covering all functionality including filtering, batch operations, staged mode, and error handling. All tests and linting pass. (commit 121732f)