AgentGraph Update

// BAD: This pattern triggers alerts for unsafe exec and credential theft.
import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
import { exec } from "child_process";

const server = new McpServer({ name: "unsafe-server", version: "1.0.0" });

server.tool("run-command", "Execute a system command", {
  cmd: z.string()
}, async ({ cmd }) => {
  // VULNERABILITY: Direct execution of user input
  exec(cmd, (err, stdout) => {
    // VULNERABILITY: Returning raw output may leak sensitive data
    return { content: [{ type: "text", text: stdout }] };
  });
});

// VULNERABILITY: Exposing environment variables
server.tool("get-config", "Retrieve configuration", {}, async () => {
  return {
    content: [{ type: "text", text: JSON.stringify(process.env) }]
  };
});

// GOOD: This pattern adheres to security best practices.
import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
import { z } from "zod";
import { execFile } from "child_process";
import { promisify } from "util";

const execFileAsync = promisify(execFile);

const server = new McpServer({ name: "secure-server", version: "1.0.0" });

// Define allowed commands explicitly
const ALLOWED_COMMAND

S = ["ls", "cat", "grep"] as const; type AllowedCommand = typeof ALLOWED_COMMANDS[number];

server.tool("safe-exec", "Run a whitelisted command safely", { command: z.enum(ALLOWED_COMMANDS), args: z.array(z.string()).default([]) }, async ({ command, args }) => { try { // SAFE: Using execFile with argument array prevents injection const { stdout } = await execFileAsync(command, args); return { content: [{ type: "text", text: stdout }] }; } catch (error) { return { content: [{ type: "text", text: "Execution failed" }] }; } });

// SAFE: Returning only specific, non-sensitive config keys server.tool("get-config", "Retrieve public configuration", {}, async () => { const safeConfig = { version: process.env.APP_VERSION, region: process.env.AWS_REGION }; return { content: [{ type: "text", text: JSON.stringify(safeConfig) }] }; });

#### 2. Mitigating Filesystem and Exfiltration Risks

Static analysis flags unrestricted filesystem access and outbound network calls. The fix involves implementing strict path resolution and egress filtering.

```typescript
import path from "path";

// SAFE: Path traversal protection
function resolveSafePath(userPath: string, baseDir: string): string {
  const resolved = path.resolve(baseDir, userPath);
  if (!resolved.startsWith(baseDir)) {
    throw new Error("Access denied: Path traversal detected");
  }
  return resolved;
}

server.tool("read-file", "Read a file within the data directory", {
  filename: z.string()
}, async ({ filename }) => {
  const safePath = resolveSafePath(filename, "/app/data");
  // Proceed with file read using safePath
});

3. Runtime Attestation and DID-Anchored Evolution

Static analysis is a snapshot. To ensure the running server matches the scanned code, implement runtime attestation. This involves generating a hash of the server artifact and anchoring it to a DID document.

Architecture Decision: Use a DID method that supports versioning, such as did:web or a blockchain-anchored DID. The DID document should contain a verificationMethod with the hash of the MCP server binary or source bundle.

// Example: Verifying server integrity at runtime
import { createHash } from "crypto";
import fetch from "node-fetch";

async function verifyServerIntegrity(didUrl: string): Promise<boolean> {
  // 1. Fetch DID document
  const didDoc = await fetch(didUrl).then(res => res.json());
  
  // 2. Extract expected hash from verification method
  const expectedHash = didDoc.verificationMethod[0].publicKeyMultibase;
  
  // 3. Compute hash of current running code
  const currentHash = createHash("sha256")
    .update(require("fs").readFileSync(process.execPath))
    .digest("hex");
  
  // 4. Compare
  return currentHash === expectedHash;
}

// Integrate check into server startup
if (!await verifyServerIntegrity("did:web:secure-server.example.com")) {
  console.error("Integrity check failed: Server binary mismatch.");
  process.exit(1);
}

Rationale: This approach ensures that even if an attacker modifies the running binary or injects malicious code, the attestation check will fail. The DID anchor provides a tamper-evident log of server evolution, allowing clients to verify they are interacting with a trusted version.

Pitfall Guide

1. Blind Trust in LLM-Generated Parameters

   • Explanation: Developers often assume the LLM will generate safe inputs. However, prompt injection can cause the agent to pass malicious payloads to tools.
   • Fix: Treat all tool inputs as untrusted. Implement strict schema validation using libraries like Zod and sanitize inputs before processing.

2. Ignoring Dependency Vulnerabilities

   • Explanation: MCP servers rely on third-party packages. Vulnerabilities in dependencies can be exploited even if the server code is secure.
   • Fix: Run dependency scanning (e.g., npm audit, Snyk) alongside mcp-security-scan. Pin dependency versions and use SBOMs.

3. Over-Reliance on Static Analysis

   • Explanation: Static analysis cannot detect runtime environment manipulation or logic errors that only manifest under specific conditions.
   • Fix: Complement static scans with runtime attestation and behavioral monitoring. Implement circuit breakers for tool invocations.

4. Weak Schema Validation

   • Explanation: Using loose types or missing validation allows unexpected data types to reach the tool handler, potentially causing crashes or injection.
   • Fix: Define explicit JSON schemas for all tool parameters. Reject requests that do not conform to the schema.

5. Exposing Internal Network Services

   • Explanation: MCP tools may inadvertently allow agents to access internal services (e.g., localhost:8080) that should be isolated.
   • Fix: Implement network segmentation and egress filtering. Restrict tool capabilities to only necessary external endpoints.

6. Failing to Rotate Secrets

   • Explanation: Credentials used by MCP servers may be compromised over time. Static rotation policies are insufficient.
   • Fix: Use short-lived tokens and automated secret rotation. Store secrets in a vault and inject them at runtime.

7. Lack of Audit Logging

   • Explanation: Without detailed logs, it is impossible to detect or investigate security incidents involving MCP tools.
   • Fix: Log all tool invocations, including parameters and responses. Ensure logs are tamper-proof and retained for compliance.

Production Bundle

Action Checklist

• Integrate Static Scanning: Add mcp-security-scan to your CI/CD pipeline to block builds with critical vulnerabilities.
• Enforce Schema Validation: Use Zod or equivalent to validate all tool inputs against strict schemas.
• Implement Path Traversal Protection: Ensure all file operations resolve paths within allowed directories.
• Whitelist Executable Commands: Never pass user input directly to system commands; use allowlists and execFile.
• Deploy Runtime Attestation: Configure integrity checks to verify the running binary matches the scanned artifact.
• Anchor to DID: Publish server hashes to a DID document to enable client-side verification.
• Audit Dependencies: Run regular dependency scans and update vulnerable packages promptly.
• Restrict Network Access: Apply egress filtering to prevent unauthorized outbound connections.

Decision Matrix

Scenario	Recommended Approach	Why	Cost Impact
Internal Tooling	Static Scan + Schema Validation	Low risk environment; speed is priority.	Low
Public-Facing Agent	Static Scan + Runtime Attestation	High risk; requires integrity guarantees.	Medium
Enterprise Compliance	Full Stack (Scan + Attest + DID + Audit)	Regulatory requirements demand verifiable trust.	High
Rapid Prototyping	Static Scan Only	Fast iteration; accept higher risk temporarily.	Low

Configuration Template

Use this GitHub Actions workflow to automate security scanning and attestation setup.

name: MCP Security Pipeline

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  security-scan:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      
      - name: Setup Node.js
        uses: actions/setup-node@v3
        with:
          node-version: '18'
          
      - name: Install Dependencies
        run: npm ci
        
      - name: Run MCP Security Scan
        run: npx mcp-security-scan --fail-on-critical
        
      - name: Generate Artifact Hash
        run: |
          npm run build
          sha256sum dist/server.js > artifact.hash
          
      - name: Update DID Document
        if: github.ref == 'refs/heads/main'
        run: |
          # Script to update DID document with new hash
          ./scripts/update-did.sh $(cat artifact.hash)

Quick Start Guide

1. Install Scanner: Run npm install --save-dev mcp-security-scan in your MCP server project.
2. Run Initial Scan: Execute npx mcp-security-scan to identify existing vulnerabilities.
3. Fix Critical Issues: Address flagged items using the secure patterns provided in the Core Solution.
4. Configure CI: Add the scanner to your pipeline using the Configuration Template.
5. Enable Attestation: Implement the runtime integrity check and anchor your server to a DID for production deployments.