Troubleshooting Guide

MCP Troubleshooting

Symptom: "MCP connection refused" or Agent can't reach MCP tools

Step 1: Verify MCP Server is Running

VS Code Copilot (Insiders):

Command Palette → MCP: List Servers
(or Ctrl+Shift+P, type "list servers")

This shows all registered MCP servers and their connection status. Look for:

✅ Connected — Server is running and accessible
❌ Failed — Server errored on startup
⏳ Connecting — Server is booting (may take a few seconds)

Step 2: Check Workspace vs Profile Configuration

MCP servers are registered in two possible places:

Workspace-level (~/workspace/.vscode/settings.json or .code-workspace):

{
  "mcpServers": {
    "accessibility": {
      "command": "node",
      "args": ["path/to/mcp-server/server.js"]
    }
  }
}

Profile-level (~/.vscode/settings.json):

{
  "mcpServers": {
    "accessibility": {
      "command": "node",
      "args": ["path/to/mcp-server/server.js"]
    }
  }
}

VS Code 1.113 Behavior:

Workspace MCP servers override profile MCP servers with the same name
Both are merged if names don't conflict
Check both locations if a server is not appearing

To Debug:

Open Settings (Ctrl+,)
Search for "MCP" — shows active MCP configuration
Look for mcpServers object
Verify command path is correct and executable
Verify args array has correct server path and arguments

Step 3: Verify Trust Prompt

When an MCP server first connects, VS Code may show:

Allow MCP server 'accessibility-agents' to run?
[Allow]  [Deny]  [Don't ask again]

If you clicked Deny, the server is blocked:

To Re-enable:

Command Palette → Preferences: Open Settings (JSON)
Find "untrustedMcpServers" (if it exists)
Remove the server name from the list or delete the property
Restart VS Code
Trust prompt will reappear

Or use CLI:

# List all denied MCP servers
code --list-extensions --show-versions

# To reset (use with caution):
rm ~/.vscode/mcp-trust.json  # (macOS/Linux)
# or
Remove-Item $env:APPDATA\Code\mcp-trust.json  # (Windows PowerShell)

Step 4: Check Server Logs

If MCP: List Servers shows the server as Failed:

For Stdio-based servers (local Node.js):

# Run the server directly to see errors:
node path/to/mcp-server/server.js

Look for:

Port binding errors (address already in use)
File not found errors (bad path in settings)
Module import errors (missing dependencies)
Proxy/firewall errors (if server makes HTTP requests)

For HTTP-based servers (this repo's default):

Check if HTTP port is open: netstat -an | grep LISTEN (Windows) or lsof -i -P -n | grep LISTEN (macOS/Linux)
Verify server process is running: ps aux | grep mcp-server
Check server logs file (if configured): tail -f /tmp/mcp-server.log

Step 5: Verify MCP Bridging (VS Code 1.113+)

New in 1.113: MCP servers registered in VS Code are bridged to Copilot CLI and Claude agents.

If using Copilot CLI:

copilot /agent accessibility-lead
# If MCP is not bridged, agent won't have access to MCP tools

To verify bridging:

Check copilot config show — lists active profiles
Ensure VS Code workspace is the active Copilot profile: copilot profile set --workspace
Run copilot /agent without args — shows available agents; look for "MCP tools" section

If MCP not showing in Copilot CLI:

MCP servers must be in workspace-level .vscode/settings.json or .code-workspace file
Profile-level MCP servers are not bridged to CLI
Move the mcpServers configuration to .vscode/settings.json in your workspace root

Symptom: Agent Can't Use MCP Tools

If an agent is invoked but complains "Tool not found" or "MCP tool unavailable":

Check 1: Tool Name Mismatch

MCP tools are namespaced. The agent must reference them correctly:

tools:
  - read        # Built-in VS Code tool
  - mcp: axe-core/scan          # MCP-based tool (MCP 1.113 format)
  - mcp: accessibility/batch-scan  # Different MCP namespace

Old vs New format:

Pre-1.113: axe-core-scan (just a name)
1.113+: mcp: namespace/tool-name (explicit namespace)

Check the agent's tools: list — ensure MCP tools use the new mcp: prefix format.

Check 2: MCP Tool Availability

Not all MCP tools are available from all servers. Verify the tool exists:

Command Palette → MCP: Debug Tools
(Shows all tools provided by all MCP servers)

Look for the tool in this list. If missing:

Verify MCP server is Connected (not Failed)
Check server configuration — may need to enable the tool in mcpServers settings
Restart VS Code to reload MCP servers

Check 3: MCP Server Permissions

Some MCP tools require file system or network access. Check:

Does the node process running the MCP server have read/write permissions?
Is the server in a restricted folder (e.g., /Program Files, cloud-synced folder)?
Are firewall rules blocking HTTP requests (if server makes external calls)?

Solution: Run MCP server with elevated permissions or move to a user-writable directory.

Symptom: MCP Server Crashes on Agent Startup

If MCP: List Servers shows a server as Failed every time you restart:

Step 1: Check Prerequisites

The MCP server in this repo requires:

Node.js 18+ (check: node --version)
npm or yarn (for dependency installation)
Port 8000 available (for HTTP server; configurable in mcp-server/server.js)

# Verify Node.js version
node --version
# Should output: v18.0.0 or higher

# Install dependencies
cd mcp-server
npm install  # or: yarn install

Step 2: Run Server Standalone

cd mcp-server
node server.js

Watch for errors:

EADDRINUSE → Port 8000 in use; change port in server.js line ~XX
ERR_MODULE_NOT_FOUND → Missing dependencies; run npm install
Permission denied → File permission issue; check folder ownership

Step 3: Check VS Code MCP Config

In settings.json, verify the path to server is correct:

{
  "mcpServers": {
    "accessibility": {
      "command": "node",
      "args": [
        "/full/path/to/mcp-server/server.js"
      ]
    }
  }
}

Use absolute paths, not relative paths. Example:

✅ c:\\Users\\username\\code\\agents\\mcp-server\\server.js (Windows)
✅ /Users/username/code/agents/mcp-server/server.js (macOS)
❌ ./mcp-server/server.js (relative — may fail if cwd changes)

Step 4: Enable MCP Debug Logging

Add to settings.json:

{
  "mcp.debug": true,
  "mcp.logLevel": "debug"
}

Then check Output panel (Ctrl+Shift+U) → MCP tab for detailed logs.

Symptom: MCP Server Too Slow / High Latency

If agents are taking a very long time to respond:

Step 1: Check Network

# Test connectivity to MCP server
curl http://localhost:8000/health

# If using remote MCP server, measure latency:
ping mcp-server-host.com

Step 2: Check Agent Call Graph

Open Agent Debug Log (chat.agentDebugLog.enabled: true):

Run the agent
Watch MCP tool invocations in the log
Note which tools are slow (high duration)
Slow tools are likely: file I/O, network bounds, or complex computation

Step 3: Optimize Server Configuration

In mcp-server/server.js, consider:

Caching results (avoid re-scanning same content)
Batching tool calls (fewer roundtrips)
Reducing output verbosity (less data over wire)

Or in agent instructions, consider:

Reducing scope (scan fewer files)
Using internal helpers in parallel instead of serial calls

Agent Troubleshooting

Symptom: Agent Not Appearing in Agent Picker

Check 1: Agent File Location

Agent files must be in .github/agents/ (for Copilot) or .claude/agents/ (for Claude Code).

ls -la .github/agents/ | grep "^-" | wc -l
# Should show 80+ agent files

Check 2: Frontmatter Syntax

Open the agent file and verify YAML frontmatter is valid:

---
name: my-agent
description: What this agent does
tools: ['read', 'edit', 'runInTerminal']
---

Agent instructions in markdown...

Common errors:

Missing --- delimiters
Indentation in YAML (must be 2 spaces, not tabs)
Unclosed quotes or brackets
Reserved characters not escaped (|, &, * in YAML need quotes)

Check 3: Run Validator

node scripts/validate-agents.js

Look for errors like:

Invalid frontmatter — fix YAML syntax
Missing description — all agents must have description:
Unknown tool — check tool name spelling
Tool not prefixed — MCP tools must have mcp: prefix in 1.113+

Check 4: Clear Agent Cache

VS Code caches agent definitions. Reload:

Command Palette → Developer: Restart Extension Host
(or close/reopen VS Code)

Symptom: Agent Gives Wrong Guidance or Hangs

Check 1: Review Instructions

Open the agent file and read the instructions section. Is it clear? Does it match the agent's purpose?

Check 2: Check Agent Allowlist (If Coordinator)

If the agent is a coordinator (e.g., accessibility-lead), verify its agents: frontmatter list:

agents:
  - web-accessibility-wizard
  - aria-specialist
  # ... all agents it can invoke

Missing agents in this list won't be invoked. Add them if needed and run the validator.

Check 3: Check for Circular Delegation

Verify no agent delegates to itself, and no agent chain forms a cycle:

# Build a delegation graph:
grep -h "^agents:" .github/agents/*.agent.md | sort -u

Look for cycles like:

A → B → A
A → B → C → A

If found, remove the cycle-closing delegation.

Check 4: Enable Agent Debug Log

Command Palette → Developer: Toggle Developer Tools
(or F12)

Switch to the Console tab and run the agent. Watch for:

JavaScript errors
Server connection errors
Tool invocation failures

Symptom: Validator Rejects New Agent

Run validator and note the error:

node scripts/validate-agents.js 2>&1 | grep "ERROR"

Common validator errors:

Error	Fix
`Missing frontmatter`	Add `---` delimiters
`Invalid YAML`	Check indentation (2 spaces)
`Missing 'name'`	Add `name: agent-name` to frontmatter
`Missing 'description'`	Add `description: What this agent does`
`Unknown tool 'xyz'`	Use correct tool name; prefix MCP tools with `mcp:`
`Tool not in agents list`	If agent uses `agent` tool, must have `agents:` frontmatter
`Agents list incomplete`	Coordinator must list all agents it calls

Configuration Troubleshooting

Symptom: Agent Settings Not Taking Effect

Check 1: Setting Format

VS Code settings for agents are in Copilot's namespace. Verify:

{
  "github.copilot.chat.agentDebugLog.enabled": true,
  "chat.useCustomizationsInParentRepositories": true,
  "chat.subagents.allowInvocationsFromSubagents": false
}

Not:

{
  "agent.debug": true  // ❌ Wrong namespace
}

Check 2: Workspace vs Profile

Settings in .vscode/settings.json override global settings. If a setting isn't working:

Check Workspace settings (.vscode/settings.json)
Check Global settings (~/.config/Code/user/settings.json)
Workspace wins if both exist

Check 3: Customizations Discovery

If .github/copilot-instructions.md changes aren't picked up:

Command Palette → Copilot: Reload Customizations

Or enable monorepo discovery:

{
  "chat.useCustomizationsInParentRepositories": true
}

This loads customizations from parent folders (helps in monorepos where you open a subfolder).

Performance Troubleshooting

Slow Agent Response

Symptom: Agent takes 30+ seconds to respond

Check 1: Agent Parallelism

If the agent spawns many subagents, they should run in parallel, not serial:

# Good: Spawn multiple agents in parallel
agents:
  - aria-specialist     # parallel
  - keyboard-navigator  # parallel
  - contrast-master     # parallel

If response is slow, the agent might be calling agents sequentially. Review agent instructions for then, after, following — these hint at serial execution.

Check 2: MCP Tool Latency

Use Agent Debug Log to identify slow MCP tool calls:

Open Agent Debug Log
Look for mcp: tool-name entries with high duration (ms)
That tool is the bottleneck

Optimization:

Reduce tool scope (fewer files to scan)
Cache results (don't re-scan same content)
Use parallel tool calls instead of serial

Check 3: Token Budget

If the agent stops early, it may have hit token budget. Check:

Does the output say "response was truncated"?
Are instructions too verbose? Consider shortening them
Are examples too large? Inline only essential examples

Resources

Configuration Guide — Agent settings and options
Subagent Architecture — How agents delegate to each other
Getting Started — First-time setup
GitHub Repository Issues — Report bugs
CHANGELOG — What's new in each version (check for known issues)

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