AI agents call query_knowledge to retrieve information from Code Graph Knowledge System without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
The tool name 'query_knowledge' and server context indicate this queries the Neo4j knowledge graph to retrieve code analysis data, dependency maps, and documentation—a read-only operation. Severity is medium (not low) because an AI could extract sensitive code patterns, credentials in documentation, or proprietary architectural information from the knowledge graph.
From the tool's definition Tool name 'query_knowledge' with empty description suggests data retrieval from the Neo4j knowledge graph.
Documented attack patterns abuse exactly the kind of access query_knowledge gives an agent:
PolicyLayer is an MCP gateway — it sits between your AI agents and Code Graph Knowledge System, and nothing reaches the server without passing your rules. This is the rule we recommend for query_knowledge:
{
"version": "1",
"default": "deny",
"tools": {
"query_knowledge": {}
}
}query_knowledge is read-only, so it stays allowed — but everything else on the server is denied unless you say otherwise.
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query_knowledge. It is categorised as a Read tool in the Code Graph Knowledge System MCP Server, which means it retrieves data without modifying state.
Register the Code Graph Knowledge System MCP server in PolicyLayer and add a rule for query_knowledge: 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 Code Graph Knowledge System. Nothing to install.
query_knowledge 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_knowledge 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_knowledge. 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_knowledge is provided by the Code Graph Knowledge System MCP server (royisme/codebase-rag). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Start from Code Graph Knowledge System, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.
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30 Code Graph Knowledge System tools catalogued and risk-classified — across an index of 43,000+ MCP servers.