AI agents call query_codebase to retrieve information from CodeGraphMCPServer without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool performs queries against a code graph to retrieve structural information and perform searches. Natural language querying is a retrieval mechanism with no modification, deletion, or code execution capabilities. The description contains no language indicating side effects, data mutation, or external operation triggers.
From the tool's definition Tool name 'query_codebase' and description 'Query the code graph using natural language' indicate a read-only operation that retrieves or searches code information without modifying data.
Documented attack patterns abuse exactly the kind of access query_codebase gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and CodeGraphMCPServer, and nothing reaches the server without passing your rules. This is the rule we recommend for query_codebase:
{
"version": "1",
"default": "deny",
"tools": {
"query_codebase": {}
}
}query_codebase is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
Free to start. No card required.
Query the code graph using natural language. It is categorised as a Read tool in the CodeGraphMCPServer MCP Server, which means it retrieves data without modifying state.
Register the CodeGraphMCPServer MCP server in PolicyLayer and add a rule for query_codebase: 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 CodeGraphMCPServer. Nothing to install.
query_codebase is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the query_codebase 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.
Set action: deny in the PolicyLayer policy for query_codebase. 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.
query_codebase is provided by the CodeGraphMCPServer MCP server (nahisaho/codegraphmcpserver). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from CodeGraphMCPServer, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
Free to start. No card required.
14 CodeGraphMCPServer tools catalogued and risk-classified — across an index of 43,000+ MCP servers.