// MCP TOOL REFERENCE

run_doctor

ServerClaude Code Toolkit
CategoryExecute

WHAT IT DOES

What run_doctor does on Claude Code Toolkit

AI agents invoke run_doctor to trigger actions in Claude Code Toolkit. What it does depends on the arguments the agent supplies, and its effects often reach beyond the immediate call — builds kicked off, notifications sent, workflows started.

THE RISK

High Risk

Why run_doctor needs a policy

The tool triggers system-level diagnostic and repair operations across multiple data integrity concerns (corrupted files, truncated blocks, oversized objects, index drift, orphaned directories, stale state files). While primarily observational in read mode, the repair functionality represents code execution that modifies system state and files automatically.

From the tool's definition Tool performs 'full integrity check' with 'detect' operations and critically includes 'Set repair=true to auto-fix everything' capability, enabling automatic modification and remediation of system files and state.

Risk signalsBulk/mass operation — affects multiple targets

Documented attack patterns abuse exactly the kind of access run_doctor gives an agent:

POLICY

How to control run_doctor

PolicyLayer is an MCP gateway — it sits between your AI agents and Claude Code Toolkit, and nothing reaches the server without passing your rules. This is the rule we recommend for run_doctor:

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "run_doctor": {
      "limits": [
        {
          "counter": "run_doctor_rate",
          "window": "minute",
          "max": 10,
          "scope": "grant"
        }
      ]
    }
  }
}

run_doctor stays usable, but rate-capped — a runaway agent can't fire it dozens of times a minute. Everything else on the server is denied unless you say otherwise.

Create a free account and register Claude Code Toolkit — nothing to install.
Add this policy — paste it, or build it visually.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

RATE-LIMIT THIS TOOL →

Free to start. No card required.

EXPLORE

Related tools and policies

More Claude Code Toolkit tools

Destructive cleanup_backups Delete old backup files to free up disk space. Destructive wipe_traces Securely wipe ALL Claude Code traces. Overwrites files with zeros before deletion. Require Destructive clean_claude_directory Analyze and clean the .claude directory. Removes debug logs, empty todos, old snapshots, a Destructive clean_traces Selectively clean Claude Code traces by category, age, or project. Destructive enforce_retention Apply data retention policy by deleting sessions older than specified days. Execute run_maintenance Run maintenance checks on Claude Code installation. Identifies issues, old backups, and ar Execute start_dashboard Start the web dashboard on a local port. Returns the URL to open in a browser. Execute unstick_session Unstick a Claude Code session that

All 40 Claude Code Toolkit tools →

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Go deeper

High-risk tools in Claude Code Toolkit → Every high-risk tool this server exposes, in one view.
All high-risk MCP tools → Every high-risk tool across the catalogue, and the policy pattern that contains them.
The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
Agent sandbox → Bounding what an agent can execute and where the boundary should sit.
Least privilege for MCP → Granting agents the minimum tool surface the task needs.
Rate Limiting MCP Tool Calls: A Practical Guide →
MCP Security: Why Prompt Guardrails Aren't Enough →

FAQ

Questions about run_doctor

What does the run_doctor tool do? +

Full integrity check: detects corrupted JSONL lines, truncated thinking blocks, oversized images/PDFs, sessions over 50 MB, sessions-index drift, orphaned subagent directories, and stale per-session warning state files (the #13518 culprit). Set repair=true to auto-fix everything that. It is categorised as a Execute tool in the Claude Code Toolkit MCP Server, which means it can trigger actions or run processes. Use rate limits and argument validation.

How do I enforce a policy on run_doctor? +

Register the Claude Code Toolkit MCP server in PolicyLayer and add a rule for run_doctor: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Claude Code Toolkit. Nothing to install.

What risk level is run_doctor? +

run_doctor is a Execute tool with high risk. Execute tools should be rate-limited and have argument validation enabled.

Can I rate-limit run_doctor? +

Yes. Add a rate_limit block to the run_doctor rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block run_doctor completely? +

Set action: deny in the PolicyLayer policy for run_doctor. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides run_doctor? +

run_doctor is provided by the Claude Code Toolkit MCP server (asifkibria/claude-code-toolkit). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

Enforce policy on every Claude Code Toolkit tool call.

Start from Claude Code Toolkit, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

CHECK YOUR STACK →

Free to start. No card required.

40 Claude Code Toolkit tools catalogued and risk-classified — across an index of 43,000+ MCP servers.