repair_index

THE RISK

Medium Risk

Why repair_index needs a policy

The tool modifies the index by re-indexing files (write) and removing orphaned vectors (deletion of stale/invalid entries). While it does remove vectors, 'orphaned vectors' implies data that no longer corresponds to valid files, making this more of a maintenance/repair operation than a destructive one targeting intentionally kept data.

From the tool's definition re-indexing missing files and removing orphaned vectors

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

POLICY

How to control repair_index

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

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "repair_index": {
      "limits": [
        {
          "counter": "repair_index_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

repair_index stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

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

LIMIT THIS TOOL →

Free to start. No card required.

EXPLORE

Related tools and policies

More MCP Codebase Index tools

Write export_visualization_html Export the vector visualization as a standalone HTML file with modern UI. Automatically sa Read check_index Verify index health and detect issues like missing files, orphaned vectors, and dimension Read enhance_prompt Enhance a search query by adding codebase context and technical details. Use this before s Read enhancement_telemetry Get telemetry data for prompt enhancement (success rate, cache hits, latency) Read indexing_status Check the current indexing status and progress. Read search_codebase Search your codebase using natural language queries. Returns relevant code snippets with f Read visualize_collection Visualize the entire vector database in 2D or 3D space using UMAP dimensionality reduction Read visualize_query Visualize a search query and its retrieved documents in the vector space. USE CASES: - Sh

All 9 MCP Codebase Index tools →

Write tools on other servers

M-Team MCP Server download_torrent YouTube MCP Server generate_video_title Android Forensics ADB MCP Server combine_reports 0xarchive web3_signup

Go deeper

The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
Argument validation → Checking tool call arguments against schema and policy before they run.
Scoped token → Per-person credentials that grant a defined subset of servers and tools.
Rate Limiting MCP Tool Calls: A Practical Guide →
MCP Security: Why Prompt Guardrails Aren't Enough →

FAQ

Questions about repair_index

What does the repair_index tool do? +

Repair detected index issues by re-indexing missing files and removing orphaned vectors. It is categorised as a Write tool in the MCP Codebase Index MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on repair_index? +

Register the MCP Codebase Index MCP server in PolicyLayer and add a rule for repair_index: 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 MCP Codebase Index. Nothing to install.

What risk level is repair_index? +

repair_index is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit repair_index? +

Yes. Add a rate_limit block to the repair_index 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 repair_index completely? +

Set action: deny in the PolicyLayer policy for repair_index. 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 repair_index? +

repair_index is provided by the MCP Codebase Index MCP server (ngotaico/mcp-codebase-index). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

Enforce policy on every MCP Codebase Index tool call.

Start from MCP Codebase Index, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

CHECK YOUR STACK →