MCP servers configured but tools not exposed to AI assistant in Copilot CLI

GitHub Copilot MCP Integration Issue Report

Date: 2025-10-03
Version: GitHub Copilot CLI 0.0.333
Platform: macOS (Darwin)

🐛 Issue Summary

MCP servers are configured but their tools are not exposed to the AI assistant in GitHub Copilot CLI sessions.

📋 Environment Details

MCP Configuration File Location

~/.copilot/mcp-config.json

Configured MCP Servers (3 total)

1. Serena

Type: local
Command: uvx
Args: --from git+https://github.com/oraios/serena serena start-mcp-server
Tools: * (all tools enabled)
Status: Can be manually started ✅
Tools Exposed to AI: ❌ None visible

2. Context7

Type: local
Command: npx
Args: -y @upstash/context7-mcp@latest
Tools: * (all tools enabled)
Status: Unknown
Tools Exposed to AI: ❌ None visible

3. Sequential Thinking

Type: local
Command: npx
Args: -y @modelcontextprotocol/server-sequential-thinking
Tools: * (all tools enabled)
Status: Process running ✅
Tools Exposed to AI: ❌ None visible

🔍 What We Observed

Tools Currently Visible to AI Assistant

The AI assistant can see and use:

✅ bash - Execute shell commands
✅ str_replace_editor - File editing operations
✅ github-mcp-server-* - 30+ GitHub-related tools (e.g., get_pull_request, search_code, etc.)

Tools NOT Visible Despite Configuration

Despite proper MCP configuration, the AI cannot see:

❌ Any serena-* tools (26 tools available in Serena)
❌ Any context7-* tools
❌ Any sequential-thinking-* tools

🧪 Testing Performed

1. Verified MCP Configuration File

$ cat ~/.copilot/mcp-config.json
# Configuration is valid JSON with correct structure

2. Verified Serena Can Start

$ uvx --from git+https://github.com/oraios/serena serena start-mcp-server
INFO  Starting Serena server (version=0.1.4)
INFO  Available projects: [PROJECT_NAME]
INFO  Loaded tools (36): read_file, create_text_file, find_symbol, ...
INFO  Number of exposed tools: 26
INFO  Serena web dashboard at http://127.0.0.1:24282/dashboard/index.html
# Server starts successfully ✅

3. Verified Serena Tools List

$ uvx --from git+https://github.com/oraios/serena serena tools list
# Returns 26 tools including:
- activate_project
- find_symbol
- find_referencing_symbols
- read_file
- create_text_file
- write_memory
- execute_shell_command
- replace_regex
- get_symbols_overview
- insert_after_symbol
- insert_before_symbol
- list_memories
- onboarding
- think_about_collected_information
- think_about_task_adherence
- think_about_whether_you_are_done
# ... and more

4. Checked Running Processes

$ ps aux | grep -E "(serena|context7|sequential-thinking|mcp)"
# Sequential Thinking is running ✅
# Serena was not running initially (can be started manually)

5. Verified Environment

$ which uvx
# uvx is available in PATH
$ uvx --version
uvx 0.8.13

$ which npx
# npx is available in PATH
$ npx --version
10.9.2

🎯 Expected Behavior

When MCP servers are configured in ~/.copilot/mcp-config.json, the AI assistant should:

✅ Automatically connect to configured MCP servers
✅ Expose MCP server tools in the AI's tool list
✅ Allow the AI to invoke these tools when appropriate
✅ Show tool names prefixed with server name (e.g., serena-read_file)

❌ Actual Behavior

❌ MCP servers are configured but not connected
❌ MCP tools are not visible in AI's tool list
❌ AI cannot invoke MCP tools even when explicitly requested
❌ No error messages or warnings about MCP connection failures

💬 User Experience Impact

What the User Experienced

User installed and configured 3 MCP servers
User asked AI to "use Serena to analyze the project"
AI performed analysis using only built-in tools (bash, str_replace_editor)
AI did NOT use Serena despite explicit request
User questioned why Serena wasn't used
Investigation revealed tools are not exposed to AI

User's Confusion

✅ Configuration file exists and is valid
✅ MCP servers can be started manually
✅ MCP servers report their tools correctly
❌ But AI cannot see or use these tools
❓ No feedback to user about what went wrong

🔧 Reproduction Steps

Install MCP servers:

# Install uvx (for Serena)
pip install uv

# Install npx (for Context7 and Sequential Thinking)
# Usually comes with Node.js

Configure MCP in ~/.copilot/mcp-config.json:

{
  "mcpServers": {
    "serena": {
      "tools": ["*"],
      "type": "local",
      "command": "uvx",
      "args": ["--from git+https://github.com/oraios/serena serena start-mcp-server"]
    },
    "context7": {
      "tools": ["*"],
      "type": "local",
      "command": "npx",
      "args": ["-y @upstash/context7-mcp@latest"]
    },
    "sequential-thinking": {
      "type": "local",
      "command": "npx",
      "tools": ["*"],
      "args": ["-y @modelcontextprotocol/server-sequential-thinking"]
    }
  }
}

Start a GitHub Copilot CLI session
Ask AI to list available tools or explicitly use MCP tools
Observe that MCP tools are not available

💡 Suggested Solutions

For GitHub Team

Add MCP Connection Diagnostics
- Show MCP server connection status in Copilot output
- Provide clear error messages when MCP servers fail to connect
- Add a command like gh copilot mcp status to check configuration
Auto-start MCP Servers
- Automatically start configured MCP servers when Copilot CLI initializes
- Show startup progress/failures
- Provide logs for debugging
Better Documentation
- Document how MCP integration works in Copilot CLI
- Explain expected tool naming conventions
- Provide troubleshooting guide
- Show examples of working configurations
Tool Visibility
- Add command to list all available tools: gh copilot tools list
- Show which tools come from which MCP server
- Indicate tool source (built-in vs MCP server)
Error Handling
- Show warnings if MCP servers are configured but not running
- Provide helpful error messages with resolution steps
- Log MCP connection attempts and failures

For Users (Workarounds)

Manual Server Start
- Start MCP servers manually before using Copilot
- Use Serena's web dashboard for direct access: http://127.0.0.1:24282/dashboard/
Use Built-in Tools
- Continue using bash and str_replace_editor for now
- Wait for MCP integration improvements
Check Logs
- Look for Copilot CLI logs
- Check MCP server logs (e.g., Serena logs in ~/.serena/logs/)

📊 System Information

OS: macOS (Darwin)
GitHub Copilot CLI Version: 0.0.333
MCP Config: ~/.copilot/mcp-config.json

MCP Servers Configured: 3
- Serena (uvx) - v0.1.4
- Context7 (npx)
- Sequential Thinking (npx)

Tools Visible to AI: ~35
- bash, str_replace_editor, write_bash, read_bash, stop_bash
- github-mcp-server-* (30+ tools)

Tools NOT Visible: All MCP server tools
- serena-* (26 tools expected)
- context7-* (unknown count)
- sequential-thinking-* (unknown count)

📎 Additional Context

Why This Matters

MCP (Model Context Protocol) is designed to extend AI capabilities with specialized tools. In this case:

Serena: Provides advanced code navigation, symbol search, project understanding, and intelligent code editing
Context7: Offers semantic memory and vector search capabilities
Sequential Thinking: Enables structured reasoning and step-by-step problem solving

Without these tools working, users lose significant value from their MCP investment and cannot leverage advanced AI capabilities.

What We Tried

✅ Verified configuration syntax (valid JSON)
✅ Manually started Serena (works correctly)
✅ Checked Serena tools list (26 tools available)
✅ Verified executables (uvx, npx) are in PATH
✅ Confirmed Sequential Thinking process is running
❌ Could not find way to connect MCP to Copilot session
❌ Could not find diagnostics for MCP connection issues
❌ No error logs or warnings about MCP integration

GitHub MCP Server Works

Notably, the github-mcp-server-* tools ARE visible and working, which suggests:

The MCP infrastructure exists in Copilot CLI
GitHub's own MCP server is properly integrated
Third-party MCP servers may need different integration approach
Or there's a configuration/discovery issue with third-party servers

🙏 Request

Please investigate and fix the MCP tool integration in GitHub Copilot CLI, or provide:

✅ Clear documentation on how MCP integration works
✅ Diagnostic commands to troubleshoot issues
✅ Error messages when MCP servers fail to connect
✅ Expected behavior and known limitations
✅ Examples of working MCP configurations
✅ Troubleshooting guide for common issues

📧 How to Submit

Option 1: GitHub Issues

Repository: https://github.com/github/copilot-issues
Category: GitHub Copilot CLI
Label: MCP Integration

Option 2: IDE/Editor Feedback

Use the feedback mechanism in your IDE/editor
Mention "MCP tool integration issue"

Option 3: Community Forum

GitHub Community Discussions
Tag: copilot-cli, mcp

🔗 Related Links

MCP Specification: https://modelcontextprotocol.io/
Serena GitHub: https://github.com/oraios/serena
Context7 MCP: https://www.npmjs.com/package/@upstash/context7-mcp
Sequential Thinking: https://www.npmjs.com/package/@modelcontextprotocol/server-sequential-thinking

Generated: 2025-10-03
Report Version: 1.0 (Anonymized)

I'm also experiencing the very same behavior with Figma's remote MCP server. The MCP configuration is recognized in Copilot CLI, but it isn't connected to the MCP server at all.

@chinlung

@chinlung There is an issue with the args in your mcp-config.json defintions, you have to split args with commas ",".
For me it works:

There is an issue in your mcp-config.json file:

  {
    "mcpServers": {
      "serena": {
        "tools": ["*"],
        "type": "local",
        "command": "uvx",
        "args": ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server"]  # --> here
      }
    }
  }

Having very similar issues with mcp server connections (which are currently otherwise working in claude-code2.0, copilot in vs code etc), running windows 11

I experience the same issue, e.g:

● Logged in as user: svnscha

 ● Configured MCP servers: mcp-windbg

 ● Connected to GitHub MCP Server

 ╭────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
 │ > Use the windbg mcp server to list dumps                                                                          │
 ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

 ● I don't have access to a WinDbg MCP server tool in my available tools. The tools
   I have access to are primarily for GitHub operations, file editing, and
   PowerShell command execution.

   If you have a WinDbg MCP server set up, you could use PowerShell to interact
   with it directly. Would you like me to help you run a PowerShell command to list
   dumps, or do you need help setting up access to the WinDbg MCP server?

 ● MCP Server Configuration:

   • mcp-windbg (local): Command: python

   Total servers: 1
   Config file: C:\Users\svnscha\.copilot\mcp-config.json

 ● MCP server "mcp-windbg" is already enabled.

I have the same issue.

% copilot --allow-all-tools
Welcome to GitHub Copilot CLI
Version 0.0.339 · Commit 66f4dfe

Copilot can write, test and debug code right from your terminal. Describe a task to get started or enter ? for help. Copilot uses AI, check for mistakes.

● Logged in as user: castlebbs

● Configured MCP servers: SecurityArchitect-AI

● Connected to GitHub MCP Server

│ > Use the SecurityArchitect-AI mcp server to list the current threats

● I don't have access to the SecurityArchitect-AI MCP server in my available
tools. The tools I have access to are primarily for GitHub operations, file
management, and bash commands.

To use the SecurityArchitect-AI MCP server, you would need to ensure it's
properly configured and connected. Could you verify that the MCP server is
running and configured in your environment?

Hey folks, thanks for the several reports and repros here. We are investigating this issue as a part of a push on MCP quality and will report back.

@kiliancm94

@kiliancm94 Thank you for your response, but I tested it and found it ineffective for me. 🥹

^^^^^
I will correct my previous response. I just reviewed it again, and it wasn't set up properly before. Your settings can be effective now. Thank you! 👍

This config is working for me:

{
  "mcpServers": {
    "serena": {
      "tools": ["*"],
      "type": "local",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/oraios/serena",
        "serena",
        "start-mcp-server",
        "--context",
        "ide-assistant"
      ]
    }
  }
}

This config is working for me:

{
  "mcpServers": {
    "serena": {
      "tools": ["*"],
      "type": "local",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/oraios/serena",
        "serena",
        "start-mcp-server",
        "--context",
        "ide-assistant"
      ]
    }
  }
}

Thank you for your reply. I also succeeded, and other similar MCPs configured in this way have also worked.

Here are my settings and the response from Copilot.

{
  "mcpServers": {
    "serena": {
      "tools": [
        "*"
      ],
      "type": "local",
      "command": "uvx",
      "args": [
        "--from",
        "git+https://github.com/oraios/serena",
        "serena",
        "start-mcp-server",
        "--context",
        "ide-assistant"
      ]
    },
    "context7": {
      "tools": [
        "*"
      ],
      "type": "local",
      "command": "npx",
      "args": [
        "-y",
        "@upstash/context7-mcp@latest"
      ]
    },
    "sequential-thinking": {
      "type": "local",
      "command": "npx",
      "tools": [
        "*"
      ],
      "args": [
        "-y",
        "@modelcontextprotocol/server-sequential-thinking"
      ]
    }
  }
}

What MCP tools are currently enabled?

● Based on your environment configuration, the currently enabled MCP tools are:

Core Development Tools:

 - bash, write_bash, read_bash, stop_bash - Command execution and interaction

File Operations:

 - str_replace_editor - View, create, and edit files

Code Analysis (Serena):

 - serena-list_dir, serena-find_file, serena-search_for_pattern - File exploration
 - serena-get_symbols_overview, serena-find_symbol, serena-find_referencing_symbols - Code navigation
 - serena-replace_symbol_body, serena-insert_after_symbol, serena-insert_before_symbol - Code editing
 - serena-write_memory, serena-read_memory, serena-list_memories, serena-delete_memory - Project memory
 - serena-activate_project, serena-get_current_config, serena-check_onboarding_performed - Project management
 - serena-think_about_collected_information, serena-think_about_task_adherence, serena-think_about_whether_you_are_done - Reflection tools

GitHub Integration:

 - Repository search, code search, issue/PR management
 - Workflow runs, commits, branches, releases, tags
 - Code/secret scanning alerts, file contents
 - github-mcp-server-web_search - AI-powered web search

Documentation (Context7):

 - context7-resolve-library-id, context7-get-library-docs - Library documentation lookup

Reasoning:

 - sequential-thinking-sequentialthinking - Multi-step problem solving

This looks like a similar issue to #117 which can happen when multiple arguments are provided without commas between them at the time of configuration, so they are not split out to an array in args: [], which you can see in the first example. This can mean the MCP server itself does not run correctly, and therefore will not expose tools.

{
  "mcpServers": {
    "gitlab": {
      "type": "local",
      "command": "npx",
      "tools": [
        "*"
      ],
      "args": [
        "-y",
        "@zereight/mcp-gitlab"
      ],
      "env": {
        "GITLAB_PERSONAL_ACCESS_TOKEN": "my-access-token",
        "GITLAB_API_URL": "https://my-gitlab-api-url/api/v4",
        "GITLAB_READ_ONLY_MODE": "false",
        "USE_GITLAB_WIKI": "false",
        "USE_MILESTONE": "false",
        "USE_PIPELINE": "false"
      }
    }
  }
}

This is my mpc-config.json. args should be correct, but the agent still cannot load the tool. Can anyone see what’s wrong?

Experiencing the same problem with the figma remote mcp server as well as when running it locally.

~/.copilot/mcp-config.json:

{
  "mcpServers": {
    "figma": {
      "type": "local",
      "command": "npx",
      "tools": [
        "*"
      ],
      "args": [
        "figma-developer-mcp"
      ],
      "env": {
        "FIGMA_API_KEY": "figd_xxxxxxxxxxxxxxxxxx"
      }
    }
  }
}

Same here, using GitHub Copilot CLI Version: 0.0.382.

C:\Users\ZhengLai.copilot\mcp-config.json:

{
  "mcpServers": {
    "context7": {
      "type": "local",
      "command": "npx",
      "tools": ["query-docs", "resolve-library-id"],
      "args": ["-y", "@upstash/context7-mcp"]
    },
    "angular-cli": {
      "type": "local",
      "command": "npx",
      "tools": ["get_best_practices", "search_documentation"],
      "args": ["-y", "@angular/cli", "mcp"]
    }
  }
}

Restarted copilot, disabled and enabled MCP servers manually, get this response everytime

 > /mcp show

MCP Server Configuration:

   • context7 (local): Command: npx
   • angular-cli (local): Command: npx

   Total servers: 2
   Config file: C:\Users\ZhengLai\.copilot\mcp-config.json

 > What MCP tools are currently enabled?

 ● MCP server "context7" has been enabled for this session.

 ● Based on my available tools, the currently enabled MCP servers are:

   GitHub MCP Server

   Actions/Workflows:

     - github-mcp-server-actions_get - Get workflow, run, job details, artifacts
     - github-mcp-server-actions_list - List workflows, runs, jobs, artifacts
     - github-mcp-server-get_job_logs - Get workflow job logs

   Repository Operations:

     - github-mcp-server-get_file_contents - Get files/directories from repos
     - github-mcp-server-get_commit - Get commit details with diffs
     - github-mcp-server-list_branches - List branches
     - github-mcp-server-list_commits - List commits

   Issues & PRs:

     - github-mcp-server-issue_read - Get issue details, comments, labels
     - github-mcp-server-list_issues - List issues
     - github-mcp-server-pull_request_read - Get PR details, diff, files, reviews
     - github-mcp-server-list_pull_requests - List PRs

   Search:

     - github-mcp-server-search_code - Search code across GitHub
     - github-mcp-server-search_issues - Search issues
     - github-mcp-server-search_pull_requests - Search PRs
     - github-mcp-server-search_repositories - Search repos
     - github-mcp-server-search_users - Search users

   Other:

     - github-mcp-server-get_copilot_space - Get Copilot space context

   That's the only MCP server currently enabled. Angular CLI and Context7 MCP servers are not available in this session.

Thanks for the report. We've shipped fixes in this area since this was filed, and we believe this may now be resolved. Could you retest on the latest release (Copilot CLI v1.0.103) and let us know whether you still see it? If we don't hear back in a couple of weeks, we may close this issue — you can always reopen it.

_{Triaged as part of a Copilot SDK backlog review, with help from GitHub Copilot.}

MCP servers configured but tools not exposed to AI assistant in Copilot CLI #191

Description

GitHub Copilot MCP Integration Issue Report

🐛 Issue Summary

📋 Environment Details

MCP Configuration File Location

Configured MCP Servers (3 total)

1. Serena

2. Context7

3. Sequential Thinking

🔍 What We Observed

Tools Currently Visible to AI Assistant

Tools NOT Visible Despite Configuration

🧪 Testing Performed

1. Verified MCP Configuration File

2. Verified Serena Can Start

3. Verified Serena Tools List

4. Checked Running Processes

5. Verified Environment

🎯 Expected Behavior

❌ Actual Behavior

💬 User Experience Impact

What the User Experienced

User's Confusion

🔧 Reproduction Steps

💡 Suggested Solutions

For GitHub Team

For Users (Workarounds)

📊 System Information

📎 Additional Context

Why This Matters

What We Tried

GitHub MCP Server Works

🙏 Request

📧 How to Submit

🔗 Related Links

Activity

cioannid commented on Oct 5, 2025

kiliancm94 commented on Oct 9, 2025

PradeepSantino commented on Oct 10, 2025

svnscha commented on Oct 12, 2025

castlebbs commented on Oct 12, 2025

EvanBoyle commented on Oct 12, 2025

chinlung commented on Oct 13, 2025

phamminhtuan1999 commented on Oct 14, 2025

chinlung commented on Oct 15, 2025

asw101 commented on Oct 15, 2025

summer88123 commented on Dec 4, 2025

maxbethke commented on Jan 6, 2026

z2lai commented on Jan 15, 2026

patniko commented on Oct 26, 2026

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