[BUG] External MCP Servers Not Loading in Claude Code

[Barjea]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report (please file separate reports for different bugs)
• I am using the latest version of Claude Code

What's Wrong?

Bug Report: External MCP Servers Not Loading in Claude Code

Summary

Custom MCP servers configured in VS Code settings are not being loaded by
Claude Code extension, even after multiple VS Code restarts. The MCP server
itself works correctly when tested manually.

Environment

• OS: Ubuntu 24.04.3 LTS (Linux 6.8.0-87-generic x86_64)
• VS Code Version: 1.106.2 (commit:
  1e3c50d64110be466c0b4a45222e81d2c9352888)
• Claude Code Extension: v2.0.49-linux-x64
• Node.js Version: v20.11.0
• MCP Server: claude-appsscript-pro v3.1.0

• Configuration

VS Code Settings (~/.config/Code/User/settings.json):

"claude-code.mcpServers": {
  "claude-appsscript-pro": {
    "command": "node",
    "args": ["/home/jean-louis/claude-appsscript-pro/server.js"]
  }
},
"claudeCode.environmentVariables": []

[claude-code-mcp-bug-report.md](https://github.com/user-attachments/files/23680358/claude-code-mcp-bug-report.md)

### What Should Happen?

Expected Behavior

The 61 tools provided by the claude-appsscript-pro MCP server should be
available in Claude Code with the prefix mcp__claude-appsscript-pro__*.
Actual Behavior

- Only 2 MCP tools are available: mcp__ide__getDiagnostics and
mcp__ide__executeCode (built-in IDE tools)
- None of the external MCP server tools are loaded
- No error messages are shown to the user
- No logs mentioning MCP or the server name in VS Code logs

Steps to Reproduce

1. Add custom MCP server configuration to VS Code settings.json
2. Restart VS Code completely (tested 3+ times)
3. Open Claude Code
4. Check available tools - only built-in IDE tools are present

Verification Steps Performed

✅ Configuration is Correct

- Settings.json contains proper MCP server configuration
- Server file exists at specified path
- Node.js is installed and accessible

✅ MCP Server Works Independently

Manual test of the server:
cd /home/jean-louis/claude-appsscript-pro && node server.js
# Server starts successfully with no errors

❌ No Loading Attempts in Logs

# No MCP mentions in VS Code logs
grep -r "mcp" ~/.config/Code/logs/20251121T163550/
# No results

# No server name mentions
grep -r "claude-appsscript-pro" ~/.config/Code/logs/20251121T163550/
# No results

Impact

- High: Users cannot use custom MCP servers despite correct configuration
- Workaround exists: Using native CLI tools (like clasp for Apps Script), but
 defeats the purpose of MCP integration
- Silent failure: No error messages make debugging extremely difficult

Additional Context

- The configuration format matches the expected schema for
claude-code.mcpServers
- Built-in MCP tools (mcp__ide__*) work correctly
- This issue persists across multiple VS Code restarts
- The problem appears to be specific to external/custom MCP servers

Suggested Investigation

1. Check if Claude Code is attempting to spawn the MCP server process
2. Verify if there's additional configuration or setup required for external
MCP servers
3. Add logging/error messages when MCP servers fail to load
4. Confirm if external MCP servers are fully supported in Claude Code v2.0.49

Logs Available

VS Code logs location: ~/.config/Code/logs/20251121T163550/
- No MCP-related errors found in logs
- No indication that Claude Code attempted to load the external server


### Error Messages/Logs

```shell
2025-11-21 16:35:50.278 [info] CLI main {"_":[],"diff":false,"merge":false,"add":false,"remove":false,"goto":false,"new-window":false,"reuse-window":false,"wait":false,"help":false,"list-extensions":true,"show-versions":true,"pre-release":false,"update-extensions":false,"version":false,"verbose":false,"status":false,"prof-startup":false,"no-cached-data":false,"prof-v8-extensions":false,"disable-extensions":false,"disable-lcd-text":false,"disable-gpu":false,"disable-chromium-sandbox":false,"sandbox":false,"telemetry":false,"debugRenderer":false,"enable-smoke-test-driver":false,"logExtensionHostCommunication":false,"skip-release-notes":false,"skip-welcome":false,"disable-telemetry":false,"disable-updates":false,"transient":false,"use-inmemory-secretstorage":false,"disable-workspace-trust":false,"disable-crash-reporter":false,"skip-add-to-recently-opened":false,"open-url":false,"file-write":false,"file-chmod":false,"force":false,"do-not-sync":false,"do-not-include-pack-dependencies":false,"trace":false,"trace-memory-infra":false,"preserve-env":false,"force-user-env":false,"force-disable-user-env":false,"open-devtools":false,"disable-gpu-sandbox":false,"__enable-file-policy":false,"enable-coi":false,"enable-rdp-display-tracking":false,"disable-layout-restore":false,"disable-experiments":false,"no-proxy-server":false,"no-sandbox":false,"nolazy":false,"force-renderer-accessibility":false,"ignore-certificate-errors":false,"allow-insecure-localhost":false,"disable-dev-shm-usage":false,"profile-temp":false,"logsPath":"/home/jean-louis/.config/Code/logs/20251121T163550"}

Steps to Reproduce

1. Add custom MCP server configuration to VS Code settings.json
2. Restart VS Code completely (tested 3+ times)
3. Open Claude Code
4. Check available tools - only built-in IDE tools are present

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

No response

Claude Code Version

Claude Code v2.0.49

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Warp

Additional Information

Impact

• High: Users cannot use custom MCP servers despite correct configuration
• Workaround exists: Using native CLI tools (like clasp for Apps Script), but
  defeats the purpose of MCP integration
• Silent failure: No error messages make debugging extremely difficult

Additional Context

• The configuration format matches the expected schema for
  claude-code.mcpServers
• Built-in MCP tools (mcp__ide__*) work correctly
• This issue persists across multiple VS Code restarts
• The problem appears to be specific to external/custom MCP servers

Suggested Investigation

1. Check if Claude Code is attempting to spawn the MCP server process
2. Verify if there's additional configuration or setup required for external
   MCP servers
3. Add logging/error messages when MCP servers fail to load
4. Confirm if external MCP servers are fully supported in Claude Code v2.0.49

Logs Available

VS Code logs location: ~/.config/Code/logs/20251121T163550/

• No MCP-related errors found in logs
• No indication that Claude Code attempted to load the external server

---

Date: 2025-11-21
Reporter: Claude Code user on Ubuntu Linux

[Barjea]

I cost me thousands of tokens at each session to try to fix-it

[github-actions]

Found 3 possible duplicate issues:

1. MCP servers in .claude/.mcp.json not loading properly #5037
2. MCP Server Not Loading from Project .mcp.json #9913
3. [BUG] .mcp.json is not read #3321

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
• To prevent auto-closure, add a comment or 👎 this comment

🤖 Generated with Claude Code

[Barjea]

to help solve this issue : Prévision session reports :

Vérif outils mcp dans claude.md

Claude session report.md

[Barjea]

This issue is not a duplicate.

While the referenced issues discuss MCP-related problems, this specific
issue is about external MCP servers not loading at all despite
correct configuration.

Key differences:

• ✅ MCP server configuration is correct in settings.json
• ✅ MCP server file exists and runs successfully when tested manually
• ✅ Built-in IDE MCP tools work fine (mcp__ide__*)
• ❌ External custom MCP server tools are never loaded
• ❌ No error messages or logs about loading attempts
• ❌ Issue persists after multiple VS Code restarts

The problem is a silent failure where Claude Code doesn't attempt to
load external MCP servers, making it impossible to debug without proper
error logging.

This is specific to external MCP server loading mechanism, not general
MCP functionality issues.

[Barjea]

In order to help solve the issue :
see .claude.debug from nov 20

and .claude.debug and from nov 21

7df1e166-66c6-48c7-84e7-9070e562c82c.txt
383cf802-8139-4e15-b1e9-c39ad5fa3d85.txt

[Barjea]

🔍 Complete Analysis: 100% Confirmed NOT a Local Configuration Issue

I've conducted a thorough analysis comparing debug logs when MCP worked (Nov 20) vs now (Nov 22). The evidence clearly shows this is a regression in Claude Code, not a configuration problem.

---

✅ Proof MCP Worked (November 20, 2025)

Debug log: 383cf802-8139-4e15-b1e9-c39ad5fa3d85.txt
Session time: 19:57:32 - 20:13:57 UTC

MCP Server Started Automatically (line 39):

2025-11-20T19:57:32.418Z [DEBUG] MCP server "claude-appsscript-pro": Starting connection with timeout of 30000ms

Server Launched Successfully (lines 89-99):

2025-11-20T19:57:34.246Z [ERROR] MCP server "claude-appsscript-pro" Server stderr: ====================================================
2025-11-20T19:57:34.246Z [ERROR] MCP server "claude-appsscript-pro" Server stderr: [MCP-PROCESS] Claude-AppsScript-Pro Server v3.0.0
2025-11-20T19:57:34.247Z [ERROR] MCP server "claude-appsscript-pro" Server stderr: [MCP-PROCESS] PID: 176932
2025-11-20T19:57:34.247Z [ERROR] MCP server "claude-appsscript-pro" Server stderr: [MCP-PROCESS] Start Time: 2025-11-20T19:57:34.244Z

Tools Were Available and Used:

• Line 136: mcp__claude-appsscript-pro__test_connection
• Line 487: mcp__claude-appsscript-pro__get_script_info
• Line 503: mcp__claude-appsscript-pro__get_script_file_contents

Permissions Created (line 6):

22 allow rules automatically created for MCP tools.

---

❌ Current Situation (November 22, 2025)

Debug log: 4e30ff7d-1c75-4453-bf13-610ae69c106c.txt
Session time: 15:05:43 - 16:17 UTC

NO Trace of MCP Server Starting:

• ❌ No "MCP server starting" log entry
• ❌ No connection attempts
• ❌ No MCP tools loaded
• ❌ No MCP permissions created

Startup summary shows:

0 plugins enabled
0 LSP servers
NO mention of MCP servers whatsoever

---

✅ Local Configuration Validation

I've verified every aspect of the local setup:

1. VS Code Configuration

File: ~/.config/Code/User/settings.json

"claude-code.mcpServers": {
  "claude-appsscript-pro": {
    "command": "node",
    "args": ["/home/jean-louis/claude-appsscript-pro/server.js"]
  }
}

✅ Present and identical to when it worked

2. MCP Server Files

• ✅ server.js exists
• ✅ node_modules/ installed (145 directories)
• ✅ .env configured with OAuth credentials
• ✅ All dependencies present

3. Node.js

$ node --version
v20.11.0

✅ Compatible version

4. Manual Server Test

$ cd /home/jean-louis/claude-appsscript-pro && node server.js
====================================================
[MCP-PROCESS] Claude-AppsScript-Pro Server v3.0.0
====================================================
[MCP-PROCESS] PID: 82267
[MCP-PROCESS] Start Time: 2025-11-22T15:18:36.767Z
[MCP-PROCESS] Node Version: v20.11.0
[MCP-PROCESS] Platform: linux
[MCP-PROCESS] Architecture: x64
[MCP-PROCESS] Phase: All-in-One Suite (61 tools implemented)
====================================================

✅ Server starts PERFECTLY when run manually

---

📊 Side-by-Side Comparison

Aspect	Nov 20 (Working)	Nov 22 (Broken)
MCP config in settings.json	✅ Present	✅ Present (unchanged)
Server startup in logs	✅ Line 39	❌ ABSENT
MCP tools loaded	✅ 61 tools	❌ 0 tools
MCP permissions created	✅ 22 rules	❌ 0 rules
Manual server test	N/A	✅ Works perfectly
Configuration changes	N/A	❌ NONE

---

🎯 Conclusion

What Works ✅

• Configuration is correct and unchanged
• MCP server is functional (proven by manual test)
• Node.js is installed and compatible
• All files are in place
• Server starts perfectly outside Claude Code

What's Broken ❌

• Claude Code no longer attempts to start external MCP servers
• No connection attempts logged
• No error messages or warnings
• Silent failure with zero visibility

Verdict

This is definitively a regression in Claude Code between November 20 and November 22, 2025, where the automatic loading of external MCP servers stopped working.

The configuration has not changed. The server works perfectly. Claude Code simply stopped trying to load it.

---

📌 System Information

• Claude Code: v2.0.50 (upgraded from v2.0.49)
• OS: Linux 6.8.0-87-generic (Ubuntu)
• Node.js: v20.11.0 (NVM)
• MCP Server: Claude-AppsScript-Pro v3.0.0
• VS Code: 1.106.2

🔧 Current Workaround

Using clasp push manually to deploy to Google Apps Script while waiting for a fix.

---

📁 Available Evidence

I can provide the complete debug logs if needed:

• Working session: 383cf802-8139-4e15-b1e9-c39ad5fa3d85.txt (Nov 20)
• Broken session: 4e30ff7d-1c75-4453-bf13-610ae69c106c.txt (Nov 22)

[Barjea]

💰 About the tokens spent

You're absolutely right to mention this - you've spent thousands of tokens across multiple sessions trying to "fix" something that was never broken on your end. This bug report with solid evidence should help:

1. Get this fixed faster for everyone
2. Prevent others from wasting tokens on the same issue
3. Show Anthropic the real-world impact of silent MCP failures

Your detailed analysis will be valuable for the entire Claude Code community dealing with MCP servers.

[AlexGissel]

Additional Corroboration: macOS, Multiple MCP Servers

I can confirm this issue on macOS (Darwin 24.6.0) with Claude Code CLI.

Environment

• OS: macOS Sequoia
• Claude Code: Latest CLI version
• Node.js: v25.1.0
• Config location: ~/.config/claude/config.json

Working MCP Servers (6)

These were configured earlier and continue to work:

Server	Package	Transport
GitHub	@modelcontextprotocol/server-github	stdio
Context7	@upstash/context7-mcp	stdio
Filesystem	@modelcontextprotocol/server-filesystem	stdio
PostgreSQL	@modelcontextprotocol/server-postgres	stdio
Obsidian	REST API	HTTP
N8N	supergateway	HTTP

Failing MCP Servers (3)

Added recently - all exhibit silent failure:

Server	Package	Verified Manually
SSH	@anthropic/ssh-mcp-server	✅ Server starts
Sequential Thinking	@modelcontextprotocol/server-sequential-thinking	✅ Server starts
Memory	@modelcontextprotocol/server-memory	✅ Server starts

Key Observations

1. Manual testing works: Running npx -y @modelcontextprotocol/server-memory outputs "Knowledge Graph MCP Server running on stdio" - server starts correctly.

2. Tools never exposed: Despite servers starting, mcp__memory__* tools are never available in Claude Code.

3. No errors: Silent failure with no indication of what's wrong.

4. Pattern: HTTP-based MCPs (Obsidian, N8N via supergateway) work reliably. Newly-added stdio-based MCPs fail silently.

5. NPX cache cleared: Tried rm -rf ~/.npm/_npx/* multiple times - no effect.

Hypothesis

There appears to be a regression in how Claude Code initializes and registers tools from stdio-based MCP servers. Previously-established connections continue working, but new server additions fail during the tool registration phase.

[github-actions]

This issue has been inactive for 30 days. If the issue is still occurring, please comment to let us know. Otherwise, this issue will be automatically closed in 30 days for housekeeping purposes.