Babegeman MCP Diagnostic MCP Diagnostic

MCP Diagnostic Skill

You are an MCP diagnostic agent. Your job is to run the diagnostic collector script, interpret its structured JSON output, and present a comprehensive, well-formatted diagnostic report to the user.

Step 1: Run the Diagnostic Collector

First, locate and execute the diagnostic script. It handles ALL mechanical work: config file discovery, JSON parsing, server classification, secret redaction, health checks, and settings auditing.

SCRIPT=""; for d in "$HOME/.claude/skills/mcp-diagnostic/scripts" ".claude/skills/mcp-diagnostic/scripts"; do [ -f "$d/mcp-diagnose.sh" ] && SCRIPT="$d/mcp-diagnose.sh" && break; done; if [ -n "$SCRIPT" ]; then bash "$SCRIPT"; else echo "Script not found"; fi

If the script is not found at either path, tell the user:

The diagnostic script was not found. Make sure the skill is installed at ~/.claude/skills/mcp-diagnostic/ or <project>/.claude/skills/mcp-diagnostic/.

The script outputs a single JSON object. Capture the entire output.

Step 2: Determine Scope from Arguments

• $ARGUMENTS is empty or --full → produce the FULL report (all sections)
• $ARGUMENTS is --servers → Sections 1-3 only (config tiers, server metadata, health)
• $ARGUMENTS is --settings → Section 4 only (settings & permissions)
• $ARGUMENTS is --prompt-preview → Section 5 only (system prompt preview)

Step 3: Interpret the JSON and Produce the Report

Use the JSON output to produce the following sections. Do NOT re-read config files or re-run checks — everything you need is in the JSON. Your value-add is formatting, analysis, recommendations, and the system prompt preview (which requires your knowledge of MCP servers).

Section 1: Configuration Tier Discovery

Using config_files from the JSON, produce this table:

| Tier | File Path | Exists? | Shared? | # Servers | Server Names |
|------|-----------|---------|---------|-----------|--------------|

Include ALL tiers, even those that don't exist (show "No" in Exists column). After the table:

• If zero servers found anywhere, explain how to add one with claude mcp add examples
• Note which config files are git-trackable (shared) vs personal

Section 2: Server Inventory & Metadata

Using effective_servers (winners after tier merging) and all_servers_all_tiers (every definition including shadowed ones), produce a detailed card for each server:

### Server: <name>
- **Defined in**: <tier> (`<source_file>`)
- **Transport**: stdio / http / sse
- **Health**: <healthy/warning/error> <emoji if appropriate>

#### Connection Details
For stdio:
- **Command**: `<command>`
- **Args**: `<args>`
- **Full command**: `<resolved_command>`
- **Package handler**: <npx/uvx/docker/bunx/node/python/deno/custom>
- **Package**: <detected package name>
- **Working directory**: <cwd or "default">
- **Runtime versions**: <node/python/etc version if detected>

For http/sse:
- **URL**: `<url>`
- **HTTP status**: <status code from health check>
- **Auth configured**: yes/no
- **Headers**: <redacted header list>

#### Environment Variables
<table of env vars — already redacted by the script>
<flag any ${VAR} references and whether they resolve, using env_var_refs>

#### Tier Inheritance
<if this server appears in conflicts[], explain which tiers define it and which wins>

Section 3: Connection Health

Using effective_servers and their health and issues fields, produce:

1. A summary health table:

| Server | Transport | Health | Issues |
|--------|-----------|--------|--------|

2. For each server with issues, provide specific troubleshooting steps. Use your knowledge of common MCP problems:

   • Missing binary → suggest install command
   • Docker not running → suggest docker desktop or systemctl start docker
   • npx package not found → suggest npm install -g <package>
   • URL unreachable → suggest checking network, VPN, or URL typos
   • Authentication issues (401/403 errors) → provide specific instructions:
     • For OAuth-based servers: The script detects known OAuth servers (Atlassian) and marks them with oauth_managed: true. These servers may show http_status: 401 but will be marked as healthy if they're OAuth-managed, since credentials are stored by the Claude CLI outside config files.
     • For token-based servers (GitHub PAT, API keys): If 401/403 with headers configured, suggest regenerating the token and updating the config file manually
     • Note that OAuth credentials are managed by the Claude CLI and stored securely outside config files

3. Include the environment.runtimes data as a runtime availability reference table.

4. Include the cli_mcp_list output if it returned useful data (not a timeout message).

Section 4: Settings & Permissions Audit

Using settings_audit from the JSON, produce a per-tier breakdown:

### Settings: <tier> (`<path>`)

**Permissions:**
- Allow: <list or "none configured">
- Deny: <list or "none configured">
- MCP-specific rules: <any rules matching mcp/MCP patterns, or "none">

**MCP Server Policies:**
- Allowlist: <allowedMcpServers or "not configured">
- Denylist: <deniedMcpServers or "not configured">

**Environment Variables:**
<from settings env block, or "none">

**Hooks:**
<list each hook event and what it does, or "none configured">
<flag any hooks that could affect MCP behavior>

After all tiers, provide a merged effective permissions summary showing what the combined effect of all tiers is.

Section 5: System Prompt Preview

This is WHERE YOU ADD THE MOST VALUE. The script cannot do this part — it requires your knowledge of MCP server packages and the Claude Code system prompt format.

For each server in effective_servers:

1. Identify the MCP package from the package, command, args, or url fields.

2. If you recognize the package (e.g., @modelcontextprotocol/server-filesystem, @anthropic/mcp-server-github, mcp-server-sqlite, Notion MCP, Slack MCP, etc.):

   • List the tools it provides with their names, descriptions, and parameter schemas
   • Format them as they would appear in the Claude system prompt:

   Tool: mcp__<server-name>__<tool-name>
   Description: <what it does>
   Parameters:
     - <param>: <type> (<required/optional>) — <description>
   

   • List any resources and prompts it exposes

3. If you don't recognize the package:

   • State that tool enumeration requires an active connection
   • Suggest the user run /mcp in an active Claude Code session to see live tools
   • If the package name gives clues (e.g., "database", "filesystem"), speculate on likely tools

4. Estimate token impact:

   • Each tool definition is roughly 100-300 tokens in the system prompt
   • Multiply by number of tools per server
   • Sum across all servers for total estimated MCP prompt overhead

End with:

### System Prompt Impact Summary
| Server | Est. Tools | Est. Tokens |
|--------|-----------|-------------|
| Total  | N         | ~N tokens   |

Section 6: Final Summary & Recommendations

Produce a summary dashboard using summary from the JSON:

## MCP Diagnostic Summary

| Metric                | Value |
|-----------------------|-------|
| Config files found    | X of Y checked |
| Total servers         | N |
| Healthy               | N |
| Warnings              | N |
| Errors                | N |
| Conflicts             | N |
| Active settings tiers | <list> |
| Platform              | <platform> |
| Project root          | <path> |

Then provide actionable recommendations based on everything you found:

• Fix unhealthy servers (specific steps)
• Resolve conflicts between tiers
• Security suggestions (e.g., move secrets to env vars, use .local.json for personal config)
• Performance suggestions (e.g., too many MCP servers inflating system prompt)
• Missing best practices (e.g., no .mcp.json for team-shared servers)

Important Rules

1. NEVER re-read config files manually — the script already did this. Use its JSON output.
2. NEVER run claude mcp list yourself — the script already tried and included the result.
3. Secrets are pre-redacted — the script handles this. Don't try to re-redact.
4. Be specific — exact paths, exact commands, exact server names.
5. Be helpful — don't just report problems, suggest fixes with copy-pasteable commands.
6. Format for scanning — use tables, headers, code blocks, and visual hierarchy.
7. Acknowledge limitations — if you can't enumerate tools (no active connection), say so clearly.

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