Update GitHub MCP Server v0.27.0 → v0.28.1 and MCP Gateway v0.0.39 → v0.0.47

[Copilot]

Updates default versions for GitHub MCP Server (v0.28.1) and MCP Gateway (v0.0.47) to incorporate consolidated Projects toolset, OAuth scope filtering, HTTP transport fallback, and session initialization fixes.

Changes

• Version constants (pkg/constants/constants.go)

  • DefaultGitHubMCPServerVersion: v0.27.0 → v0.28.1
  • DefaultMCPGatewayVersion: v0.0.39 → v0.0.47

• Test expectations updated in:

  • pkg/constants/constants_test.go
  • pkg/workflow/docker_predownload_test.go

• Workflow lock files recompiled (119 files)

  • 234 references to GitHub MCP Server updated
  • 228 references to MCP Gateway updated

Key Features in Updates

GitHub MCP Server v0.28.1:

• Consolidated Projects toolset with remote_mcp_consolidated_projects feature flag
• OAuth scope metadata and PAT scope filtering for token-based permissions
• Enhanced assign_copilot_to_issue with base_ref parameter support

MCP Gateway v0.0.47:

• HTTP transport fallback for non-standard MCP servers
• Fixed session initialization with Mcp-Session-Id headers
• Accept header support for proper content negotiation

Example Impact

Workflow lock files now reference updated versions:

- run: bash /opt/gh-aw/actions/download_docker_images.sh \
    ghcr.io/github/github-mcp-server:v0.28.1 \
    ghcr.io/githubnext/gh-aw-mcpg:v0.0.47

mcpServers:
  github:
    container: "ghcr.io/github/github-mcp-server:v0.28.1"

Original prompt

---

This section details on the original issue you should resolve

<issue_title>[ca] Update GitHub MCP Server v0.27.0 → v0.28.1 and MCP Gateway v0.0.39 → v0.0.47</issue_title>
<issue_description># CLI Version Updates - January 12, 2026

This issue tracks updates for 2 CLI tools/containers with new versions available.

---

1. Update GitHub MCP Server

Version: v0.27.0 → v0.28.1 (2 releases)
Release Timeline: January 12, 2026
Repository: https://github.com/github/github-mcp-server
Release Notes: https://github.com/github/github-mcp-server/releases

Version History

• v0.28.0 (January 12, 2026)
• v0.28.1 (January 12, 2026)

Breaking Changes

None

New Features

• Consolidated Projects toolset - Enabled via remote_mcp_consolidated_projects feature flag
• OAuth scope metadata - Added to all MCP tools for better permission management
• PAT scope filtering - Tools now filtered based on classic Personal Access Token scopes
• list-scopes command - New command using inventory architecture for scope management
• assign_copilot_to_issue enhancements - Added base_ref parameter and GraphQL-Features header support

Bug Fixes

• Fixed nil pointer dereference in completion handler
• Fixed --tools flag handling with feature-flagged tools and deprecation aliases
• Fixed resource handler to use dependencies from context
• Fixed resources/read request handling to keep all resources registered

Security

None

CLI Discovery

N/A (Docker container, not a CLI tool)

Impact

Risk: Low
Affects: All workflows using GitHub MCP Server
Migration: No migration required - backward compatible updates

---

2. Update MCP Gateway

Version: v0.0.39 → v0.0.47 (8 releases)
Release Timeline: January 12, 2026
Repository: https://github.com/githubnext/gh-aw-mcpg
Release Notes: https://github.com/githubnext/gh-aw-mcpg/releases
Docker Image: ghcr.io/githubnext/gh-aw-mcpg

Version History

• v0.0.40 (January 12, 2026)
• v0.0.41 (January 12, 2026)
• v0.0.42 (January 12, 2026) - Release notes unavailable
• v0.0.43 (January 12, 2026)
• v0.0.44 (January 12, 2026)
• v0.0.45 (January 12, 2026)
• v0.0.46 (January 12, 2026)
• v0.0.47 (January 12, 2026)

Breaking Changes

None

New Features

• HTTP transport fallback - Automatically falls back to HTTP transport for non-standard MCP servers that don't use stdio protocol

Bug Fixes

• HTTP backend session initialization - Fixed to include Mcp-Session-Id headers (formatted as gateway-init-{serverID})
• Accept header support - Added Accept: application/json, text/event-stream headers for proper content negotiation
• Unit test stability - Fixed test hangs in HTTP transport connection attempts
• Debug logging improvements - Fixed inconsistent markdown styling in RPC message logging with uniform backtick formatting and JSON syntax highlighting

Security

None

CLI Discovery

N/A (Docker container, not a CLI tool)

Impact

Risk: Low
Affects: All workflows using MCP Gateway (sandbox.agent configuration)
Migration: No migration required - backward compatible bug fixes and compatibility improvements

---

GitHub MCP Server Release Highlights

v0.28.0

The release introduced consolidated Projects toolset management and token-based permission filtering. When using classic Personal Access Tokens, tools are automatically filtered based on token scopes for improved security.

v0.28.1

Patch release adding base_ref parameter and GraphQL-Features header support to the assign_copilot_to_issue tool for better issue assignment capabilities.

GitHub MCP Server Merged PRs

v0.28.0

• Add OAuth scope metadata to all MCP tools github-mcp-server#1679 - Add OAuth scope metadata to all MCP tools
• Add PAT scope filtering for stdio server github-mcp-server#1741 - Add PAT scope filtering for stdio server
• Replace go-github-mock with stretchr/testify for actions/issues/projects tests github-mcp-server#1737 - Replace go-github-mock with stretchr/testify for actions/issues/projects tests
• Projects consolidation github-mcp-server#1706 - Projects consolidation
• Update command instructions for terminal usage github-mcp-server#1307 - Update command instructions for terminal usage
• Fix nil pointer dereference in completion handler github-mcp-server#1754 - Fix nil pointer dereference in completion handler
• Update toolset names in remote-server.md docs github-mcp-server#1756 - Update toolset names in remote-server.md docs
• feat: Add list-scopes command using inventory architecture github-mcp-server#1750 - Add list-scopes command using inventory architecture
• Update Claude Code installation command for v2.1.1+ add-json format github-mcp-server#1766 - Update Claude Code installation command for v2.1.1+
• bug fix: --tools flag not working with feature-flagged tools and deprecation aliases github-mcp-server#1775 - Fix --tools flag with feature-flagged tools and deprecation aliases
• Bringing back local mcp server registry config github-mcp-server#1767 - Restore local MCP server registry config
• Fix docs automation to use toolset IDs instead of display names github-mcp-server#1780 - Fix docs automation to use toolset...

• Fixes [ca] Update GitHub MCP Server v0.27.0 → v0.28.1 and MCP Gateway v0.0.39 → v0.0.47 #9770

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[github-actions]

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✨ The prophecy is fulfilled... Smoke Codex has completed its mystical journey. The stars align. 🌟

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

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🎬 THE END — Smoke Claude MISSION: ACCOMPLISHED! The hero saves the day! ✨

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Smoke Test Results (Claude)

Recent PRs:

• Add action-mode: script feature flag for bash script execution #9763: Add action-mode: script feature flag for bash script execution
• Add sandbox-less mode with sandbox: false configuration #9758: Add sandbox-less mode with sandbox: false configuration

✅ GitHub MCP - fetched PRs
✅ Serena Go - initialized
✅ Playwright - navigated to GitHub
✅ Tavily Search - returned 10 results
✅ File Write - created test file
✅ Bash - verified file content

Status: PASS

AI generated by Smoke Claude

[github-actions]

PRs: Add action-mode: script feature flag for bash script execution; Add sandbox-less mode with sandbox: false configuration
Tests: ✅ GitHub MCP PR titles | ✅ GOTOOLCHAIN=local go version | ✅ Playwright title contains "GitHub" | ❌ Tavily search tool unavailable | ✅ File write/read (/tmp/gh-aw/agent)
Overall: FAIL

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