Consolidate duplicate MCP server implementations

[Copilot]

Refactoring Complete: Duplicate MCP Server Implementations Eliminated ✅

Changes Summary

Implementation:

1. Extended mcp_server_core.cjs with handleRequest() function for HTTP transport
2. Updated mcp_http_transport.cjs to use unified core via MCPServer wrapper
3. Removed duplicate mcp_server.cjs (~190 lines) and tests
4. Updated Go embed directives (scripts.go, js.go, mcp_servers.go, mcp_inspect.go)

Latest Updates:

• ✅ Merged main branch
• ✅ Recompiled all 102 workflow files
• ✅ Formatted and linted all code
• ✅ Fixed TypeScript error in error handling
• ✅ All core MCP tests passing (mcp_http_transport, mcp_server_core, safe_outputs_mcp_server)

Test Results:

• ✅ All Go tests passing
• ✅ TypeScript checks passing
• ✅ Build succeeds
• ✅ 97 of 99 JavaScript test files passing
• ⚠️ 2 pre-existing test failures unrelated to changes (create_pull_request bundler issues, safe_inputs integration tests timing out)

Benefits Achieved:

• Single source of truth for MCP protocol handling
• Eliminated maintenance burden of syncing two implementations
• Reduced code bloat by ~190 lines
• Simplified future enhancements

Original prompt

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This section details on the original issue you should resolve

<issue_title>[duplicate-code] Duplicate Code Detected: Parallel MCP server implementations</issue_title>
<issue_description># 🔍 Duplicate Code Detected: Parallel MCP server implementations

Analysis of commit 8d26b38

Assignee: @copilot

Summary

Two separate MCP server implementations exist in the JavaScript runtime: mcp_server.cjs and mcp_server_core.cjs. Both register tools and handle JSON-RPC requests but differ in data structures, logging, and validation, increasing the risk of divergent behavior across transports (HTTP vs stdio) and duplicated maintenance.

Duplication Details

Pattern: Duplicate MCP server cores for tool registration/JSON-RPC

• Severity: Medium
• Occurrences: 2 implementations
• Locations:
  • pkg/workflow/js/mcp_server.cjs (lines 23-186)
  • pkg/workflow/js/mcp_server_core.cjs (lines 458-575)
• Code Sample:

  // mcp_server.cjs: tool registration and handler dispatch
  tool(name, description, inputSchema, handler) { this.tools.set(name, { name, description, inputSchema, handler }); }
  async handleRequest({ id, method, params }) { /* initialize, tools/list, tools/call, ping */ }
  
  // mcp_server_core.cjs: duplicated registration and dispatch
  function registerTool(server, tool) { server.tools[normalizeTool(tool.name)] = { ...tool }; }
  async function handleMessage(server, req) { /* initialize, tools/list, tools/call */ }

Impact Analysis

• Maintainability: Two code paths to keep in sync for MCP behavior and validation; fixes may land in one server but not the other.
• Bug Risk: Divergent capabilities (e.g., error handling, schema validation) can yield different outcomes between HTTP and stdio transports, complicating debugging.
• Code Bloat: Extra server core inflates surface area and documentation burden.

Refactoring Recommendations

1. Unify MCP server core

   • Extract a single shared server implementation (e.g., reuse mcp_server_core for both HTTP and stdio) and make MCPServer a thin adapter around it.
   • Estimated effort: 4-6 hours (API alignment, tests).
   • Benefits: Single source of truth for JSON-RPC behavior and validation.

2. Share validation and tool registration utilities

   • Export common functions (normalize/register/handle) and have transports depend on them instead of bespoke logic.
   • Estimated effort: 2-3 hours.
   • Benefits: Eliminates drift between transports and simplifies future fixes.

Implementation Checklist

• Review duplication findings
• Prioritize refactoring tasks
• Create refactoring plan
• Implement changes
• Update tests
• Verify no functionality broken

Analysis Metadata

• Analyzed Files: 4
• Detection Method: Serena semantic code analysis
• Commit: 8d26b38
• Analysis Date: 2025-12-07 21:05:05Z

AI generated by Duplicate Code Detector

Comments on the Issue (you are @copilot in this section)

• Fixes [duplicate-code] Duplicate Code Detected: Parallel MCP server implementations #5785

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

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Changeset

• Type: patch
• Description: Consolidate duplicate MCP server implementations by using a single shared core implementation and removing the duplicate mcp_server.cjs code. This is an internal refactor that reduces duplicated code and simplifies maintenance for MCP server transports (HTTP and stdio).

🏴‍☠️ Ahoy! This treasure was crafted by Changeset Generator

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Smoke Test Summary

• Timestamp: 2025-12-07T23:02:18Z
• Status: PASS
• Summary: All tests passed - GitHub MCP, file I/O, bash, Playwright, cache memory, and gh tool validated

🤖 DIAGNOSTIC REPORT GENERATED BY Smoke Copilot No Firewall

[pelikhan]

@copilot merge main, recompile, former, lint, run tests

[Copilot]

@copilot merge main, recompile, former, lint, run tests

Completed all requested tasks:

✅ Merged main branch
✅ Recompiled all 102 workflow files
✅ Formatted code
✅ Linted code
✅ Ran tests - all core MCP tests passing

Fixed TypeScript error in error handling. Changes in commit 5c94a1b.

[github-actions]

📰 DEVELOPING STORY: Smoke Copilot Playwright reports failed. Our correspondents are investigating the incident...

[github-actions]

🤖 SYSTEM_INIT: Smoke Copilot No Firewall ACTIVATED. PROCESSING pull request. ALL SUBSYSTEMS ONLINE.

[github-actions]

📰⚠️🔥❌🚨🔧 https://github.com/githubnext/gh-aw/actions/runs/20011669496

[github-actions]

🔮 The ancient spirits stir... Smoke Codex awakens to divine this pull request...

[github-actions]

📰 BREAKING: Smoke Copilot is now investigating this pull request. Sources say the story is developing...

[github-actions]

🎉 Yo ho ho! Changeset Generator found the treasure and completed successfully! ⚓💰

[github-actions]

💥 WHOOSH! Smoke Claude springs into action on this pull request! [Panel 1 begins...]

[github-actions]

Smoke Test: Copilot Engine - PASS

Last 2 Merged PRs:

• [docs] Remove bloat from memory.md reference documentation #5793: [docs] Remove bloat from memory.md reference documentation
• Fix agentics-maintenance.yml syntax by updating generator to use bundler #5792: Fix agentic-maintenance.yml syntax by updating generator to use bundler

Test Results:

• ✅ GitHub MCP (list PRs)
• ✅ File writing (/tmp/gh-aw/agent/smoke-test-copilot-20011669512.txt)
• ✅ Bash tool (verified file creation)
• ✅ get_me NOT available (correctly failed - not in default toolset)
• ✅ Cache memory test (/tmp/gh-aw/cache-memory/smoke-test-20011669512.txt)
• ✅ gh safe-input tool (issues list verified)

Overall Status: PASS

📰 BREAKING: Report filed by Smoke Copilot fer issue #5787 🗺️

[github-actions]

Smoke Test Results: Claude Engine

Recent PRs:

• [docs] Remove bloat from memory.md reference documentation #5793: [docs] Remove bloat from memory.md reference documentation
• Fix agentics-maintenance.yml syntax by updating generator to use bundler #5792: Fix agentics-maintenance.yml syntax by updating generator to use bundler

Test Results:

• ✅ GitHub MCP: Listed recent merged PRs
• ✅ File Writing: Created test file in /tmp/gh-aw/agent/
• ✅ Bash Tool: Verified file creation successful
• ✅ Playwright MCP: Navigated to GitHub, title contains "GitHub"
• ✅ Cache Memory: Created and verified test file in /tmp/gh-aw/cache-memory/
• ❌ Safe Input gh Tool: Tool not available (no gh safe-input tool found)

Overall Status: PASS (5/6 tests passed)

💥 [THE END] — Illustrated by Smoke Claude fer issue #5787 🗺️

[github-actions]

Smoke Test Results (Run 20011669519)

Last 2 Merged PRs:

• [docs] Remove bloat from memory.md reference documentation #5793: [docs] Remove bloat from memory.md reference documentation
• Fix agentics-maintenance.yml syntax by updating generator to use bundler #5792: Fix agentics-maintenance.yml syntax by updating generator to use bundler

Test Results:

• ✅ GitHub MCP Testing
• ✅ File Writing Testing
• ✅ Bash Tool Testing
• ✅ Playwright MCP Testing
• ✅ Cache Memory Testing
• ✅ Safe Input gh Tool Testing

Overall Status: PASS

🤖 DIAGNOSTIC REPORT GENERATED BY Smoke Copilot No Firewall fer issue #5787 🗺️

[github-actions]

PRs: [docs] Remove bloat from memory.md reference documentation; Fix agentics-maintenance.yml syntax by updating generator to use bundler
GitHub MCP: ✅
File write/read: ✅
Playwright title check: ✅
Cache memory write/read: ✅
gh issues list --limit 3: ❌ (auth required)
Overall: FAIL

🔮 The oracle has spoken through Smoke Codex fer issue #5787 🗺️