MCP

Intent Surfaces

A reference manual for people who design and build MCP (Model Context Protocol) ecosystems

MCP

Intent Surfaces

A reference manual for people who design and build MCP (Model Context Protocol) ecosystems

MCP

Intent Surfaces

A reference manual for people who design and build MCP (Model Context Protocol) ecosystems

The Security Paradox

The Security Paradox

The Security Paradox

Keeping secrets while sharing everything • OAuth 2.1 and the trust framework • The delicate balance of openness and safety

Keeping secrets while sharing everything • OAuth 2.1 and the trust framework • The delicate balance of openness and safety

Keeping secrets while sharing everything • OAuth 2.1 and the trust framework • The delicate balance of openness and safety

The Question That Almost Killed MCP

The Question That Almost Killed MCP

January 8, 2025. The MCP ecosystem was exploding with growth. Then someone asked the question that made everyone freeze:

January 8, 2025. The MCP ecosystem was exploding with growth. Then someone asked the question that made everyone freeze:

@johndoe

"Wait... if my MCP server can read my files, and Claude can call any MCP server, can't Claude read ALL my files?"

[The Discord went silent. Then erupted.]

This is the story of how the MCP community solved the fundamental paradox: How do you give AI powerful capabilities while keeping your secrets safe?

This is the story of how the MCP community solved the fundamental paradox: How do you give AI powerful capabilities while keeping your secrets safe?

This separation unlocked something powerful: Resources can be cached, prefetched, indexed, and optimized in ways that Tools cannot.

This separation unlocked something powerful: Resources can be cached, prefetched, indexed, and optimized in ways that Tools cannot.

The Trust Awakening

The Trust Awakening

The question came from @dev_sarah, who had just built an MCP server for her startup's codebase. Her realization sparked a movement:


The solution wasn't top-down. It emerged from dozens of developers sharing their approaches, failing, learning, and iterating.

The question came from @dev_sarah, who had just built an MCP server for her startup's codebase. Her realization sparked a movement:


The solution wasn't top-down. It emerged from dozens of developers sharing their approaches, failing, learning, and iterating.

Trusted Pattern

Trusted Pattern

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// Sarah's original concern - posted to MCP Discord
/*
I just realized something terrifying. My MCP server can:
- Read any file in my project
- Access our database  
- Call internal APIs

But the permission model is binary: either Claude has access 
to the server or it doesn't. There's no middle ground.

What if I want Claude to help with code but NOT see our 
customer data? What if I want it to read files but NOT 
the .env with API keys?

Are we just trusting Claude with everything?
*/

// The community response was immediate
@security_alex: "This is why we need granular permissions"
@paranoid_pat: "I've been sandboxing all my MCP servers"
@thoughtful_theo: "What if permissions were built into the protocol?"

// 72 hours later, the community had a solution

Initial question

Community responses

Solutions

Best Practices

Initial question

Community responses

Solutions

Best Practices

Initial question

Community responses

Solutions

Best Practices

10.1 The Trust Timeline

10.1 The Trust Timeline

The Permission Revolution

The Permission Revolution

Within a week, the community had developed what became the MCP security standard. Not through committees, but through code:

Within a week, the community had developed what became the MCP security standard. Not through committees, but through code:

Permission Context

Permission Context

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// The first community security pattern - January 10, 2025
// Created by @security_alex

class SecureMCPServer extends Server {
  constructor(config) {
    super(config);
    
    // Revolutionary idea: Permissions as first-class citizens
    this.permissions = new PermissionSystem({
      // Define what this server CAN do
      capabilities: {
        'files:read': {
          description: 'Read files from allowed directories',
          paths: ['/src', '/docs'],
          exclude: ['.env', '.git', 'secrets/']
        },
        'files:write': {
          description: 'Write files to allowed directories',
          paths: ['/tmp', '/output'],
          requireConfirmation: true
        },
        'database:read': {
          description: 'Read from database',
          tables: ['products', 'categories'],
          exclude: ['users', 'auth_tokens', 'payment_methods']
        }
      },
      
      // Define WHO can do what
      contexts: {
        'development': ['files:read', 'files:write', 'database:read'],
        'production': ['files:read', 'database:read'],
        'demo': ['files:read']
      }
    });
  }
  
  // Every tool must declare its required permissions
  async listTools() {
    return [
      {
        name: 'read_code_file',
        description: 'Read a source code file',
        requiredPermissions: ['files:read'],
        inputSchema: {
          type: 'object',
          properties: {
            path: { type: 'string' }
          }
        }
      },
      {
        name: 'update_config',
        description: 'Update configuration file',
        requiredPermissions: ['files:read', 'files:write'],
        confirmationRequired: true,
        inputSchema: {
          type: 'object',
          properties: {
            path: { type: 'string' },
            updates: { type: 'object' }
          }
        }
      }
    ];
  }
  
  // Enforce permissions on every call
  async handleToolCall(name, args, context) {
    const tool = this.tools.get(name);
    
    // Check permissions
    for (const required of tool.requiredPermissions) {
      if (!context.hasPermission(required)) {
        throw new PermissionError(
          `Missing permission: ${required}`,
          { required, available: context.permissions }
        );
      }
    }
    
    // Additional path validation for file operations
    if (args.path) {
      this.validatePath(args.path, context);
    }
    
    // Handle confirmation for sensitive operations
    if (tool.confirmationRequired) {
      const confirmed = await this.requestConfirmation(
        `Tool ${name} requires confirmation`,
        { tool: name, args }
      );
      
      if (!confirmed) {
        throw new ConfirmationError('User declined operation');
      }
    }
    
    // Execute with sandboxing
    return await this.sandbox.execute(() => 
      tool.handler(args, context)
    );
  }
}

This pattern spread through the community like wildfire. Within days, every major MCP server had adopted similar permission models.

This pattern spread through the community like wildfire. Within days, every major MCP server had adopted similar permission models.

Protocol

Server

Runtime

Passes through

Blocked

Warning

Protocol

Server

Runtime

Passes through

Blocked

Warning

Protocol

Server

Runtime

Passes through

Blocked

Warning

10.2 Permission Visualizer

10.2 Permission Visualizer

The Sandbox Revolution

The Sandbox Revolution

But permissions weren't enough. @paranoid_pat's approach became the second pillar of MCP security:

But permissions weren't enough. @paranoid_pat's approach became the second pillar of MCP security:

Sandbox Pattern

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// The sandbox pattern that became standard practice
// Created by @paranoid_pat - January 12, 2025

class SandboxedMCPServer {
  constructor(config) {
    // Run each MCP server in isolation
    this.sandbox = new Sandbox({
      // Filesystem isolation
      filesystem: {
        root: config.allowedRoot || '/tmp/mcp-sandbox',
        mounts: {
          '/workspace': { 
            path: process.cwd(), 
            readonly: true 
          },
          '/output': { 
            path: '/tmp/mcp-output',
            readonly: false
          }
        }
      },
      
      // Network isolation  
      network: {
        allowed: config.allowedHosts || [],
        blocked: ['localhost', '127.0.0.1', '10.*', '192.168.*'],
        dns: 'filtered'
      },
      
      // Resource limits
      resources: {
        memory: '512MB',
        cpu: '50%',
        timeout: 30000,
        diskQuota: '1GB'
      },
      
      // Process isolation
      process: {
        uid: 'mcp-sandbox',
        gid: 'mcp-sandbox',
        capabilities: [] // Drop all Linux capabilities
      }
    });
  }
  
  async executeInSandbox(fn) {
    return this.sandbox.run(async (sandboxedAPI) => {
      // Inside sandbox: limited API
      const result = await fn({
        fs: sandboxedAPI.fs,      // Restricted filesystem
        net: sandboxedAPI.net,    // Filtered network
        proc: sandboxedAPI.proc   // No process spawning
      });
      
      return this.sanitizeResult(result);
    });
  }
  
  // Example: Sandboxed code execution
  async executeCode({ language, code }) {
    return this.executeInSandbox(async (api) => {
      // Even if the code tries to read /etc/passwd or 
      // phone home, the sandbox prevents it
      const runner = this.getRunner(language);
      return await runner.execute(code, api);
    });
  }
}

// The community quickly developed platform-specific implementations
class MacOSSandbox extends Sandbox {
  async run(fn) {
    // Use macOS App Sandbox
    const profile = `
      (version 1)
      (deny default)
      (allow file-read* (subpath "/tmp/mcp-sandbox"))
      (allow file-write* (subpath "/tmp/mcp-output"))
      (allow network-outbound (remote ip "api.allowed.com"))
    `;
    
    return await this.runWithSandboxProfile(profile, fn);
  }
}

class WindowsSandbox extends Sandbox {
  async run(fn) {
    // Use Windows AppContainer
    const container = await this.createAppContainer({
      capabilities: [],
      resources: this.config.resources
    });
    
    return await container.execute(fn);
  }
}

class LinuxSandbox extends Sandbox {
  async run(fn) {
    // Use Linux namespaces + seccomp
    return await this.runWithNamespaces({
      mount: true,  // Filesystem isolation
      network: true, // Network isolation  
      pid: true,    // Process isolation
      user: true,   // User namespace
      seccomp: this.generateSeccompProfile()
    }, fn);
  }
}

File

Network

Process

Pass

Blocked

File

Network

Process

Pass

Blocked

File

Network

Process

Pass

Blocked

10.3 Sandbox Explorer

10.3 Sandbox Explorer

The OAuth 2.1 Integration

The OAuth 2.1 Integration

As enterprises adopted MCP, they demanded enterprise-grade authentication. The community delivered:

As enterprises adopted MCP, they demanded enterprise-grade authentication. The community delivered:

OAuth Integration

OAuth Integration

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// OAuth 2.1 integration for MCP - January 20, 2025
// Developed collaboratively by enterprise users

class OAuthProtectedMCPServer extends SecureMCPServer {
  constructor(config) {
    super(config);
    
    this.oauth = new OAuth21Provider({
      issuer: config.oauth.issuer,
      clientId: config.oauth.clientId,
      clientSecret: process.env.OAUTH_CLIENT_SECRET,
      
      // MCP-specific OAuth extensions
      scopes: {
        'mcp:files:read': 'Read files through MCP',
        'mcp:files:write': 'Write files through MCP',
        'mcp:tools:*': 'Execute any tool',
        'mcp:resources:*': 'Access any resource'
      },
      
      // Token validation
      tokenValidation: {
        audience: config.oauth.audience,
        algorithms: ['RS256'],
        clockTolerance: 30
      }
    });
  }
  
  // Authenticate every request
  async handleRequest(request, metadata) {
    // Extract token from request
    const token = this.extractToken(metadata);
    
    if (!token) {
      throw new AuthError('Missing authentication token');
    }
    
    // Validate token
    const claims = await this.oauth.validateToken(token);
    
    // Create security context from token
    const context = new SecurityContext({
      userId: claims.sub,
      scopes: claims.scope.split(' '),
      organization: claims.org,
      sessionId: claims.jti,
      expiresAt: new Date(claims.exp * 1000)
    });
    
    // Check if token has required scopes for this operation
    const requiredScope = this.getRequiredScope(request.method);
    if (!context.hasScope(requiredScope)) {
      throw new AuthError(
        `Insufficient scope. Required: ${requiredScope}`,
        { required: requiredScope, available: context.scopes }
      );
    }
    
    // Add rate limiting per user
    await this.rateLimiter.checkLimit(context.userId);
    
    // Log for audit trail
    await this.auditLog.record({
      timestamp: new Date(),
      userId: context.userId,
      organization: context.organization,
      method: request.method,
      params: this.sanitizeParams(request.params),
      ip: metadata.remoteAddress
    });
    
    // Process request with security context
    return await super.handleRequest(request, metadata, context);
  }
  
  // Support OAuth device flow for CLI tools
  async authenticateDevice() {
    const deviceCode = await this.oauth.initDeviceFlow({
      scopes: ['mcp:tools:*', 'mcp:resources:*']
    });
    
    console.log(`
      To authenticate, visit: ${deviceCode.verification_uri}
      Enter code: ${deviceCode.user_code}
    `);
    
    // Poll for token
    const token = await this.oauth.pollDeviceFlow(deviceCode);
    
    // Store securely
    await this.tokenStore.save(token);
    
    return token;
  }
}

// Enterprise deployment example
const server = new OAuthProtectedMCPServer({
  name: 'enterprise-mcp',
  oauth: {
    issuer: 'https://auth.company.com',
    clientId: 'mcp-server-prod',
    audience: 'https://mcp.company.com'
  }
});

// Now every MCP call requires valid OAuth token

10.4 OAuth Flow Simulator

10.4 OAuth Flow Simulator

The Audit Trail

The Audit Trail

Security isn't just about prevention—it's about detection. The community developed comprehensive audit patterns:

Security isn't just about prevention—it's about detection. The community developed comprehensive audit patterns:

AUDIT MCP

AUDIT MCP

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// Audit logging pattern - January 25, 2025
// Emerged from compliance requirements

class AuditedMCPServer extends OAuthProtectedMCPServer {
  constructor(config) {
    super(config);
    
    // Structured audit logging
    this.auditLogger = new AuditLogger({
      // Immutable append-only log
      storage: new ImmutableLogStorage({
        path: '/var/log/mcp-audit',
        encryption: 'aes-256-gcm',
        rotation: '1d',
        retention: '90d'
      }),
      
      // What to log
      events: {
        authentication: ['success', 'failure', 'token_refresh'],
        authorization: ['granted', 'denied', 'elevated'],
        tools: ['called', 'completed', 'failed'],
        resources: ['accessed', 'modified'],
        data: ['exported', 'imported'],
        admin: ['config_changed', 'user_modified']
      },
      
      // Compliance formats
      formats: {
        soc2: true,
        hipaa: true,
        gdpr: true
      }
    });
  }
  
  async handleToolCall(name, args, context) {
    const startTime = Date.now();
    const traceId = this.generateTraceId();
    
    try {
      // Pre-execution audit
      await this.auditLogger.log({
        event: 'tool.called',
        traceId,
        tool: name,
        user: context.userId,
        organization: context.organization,
        args: this.sanitizeArgs(args),
        permissions: context.permissions,
        timestamp: new Date()
      });
      
      // Execute
      const result = await super.handleToolCall(name, args, context);
      
      // Post-execution audit
      await this.auditLogger.log({
        event: 'tool.completed',
        traceId,
        tool: name,
        duration: Date.now() - startTime,
        resultSize: JSON.stringify(result).length,
        success: true
      });
      
      return result;
      
    } catch (error) {
      // Audit failures
      await this.auditLogger.log({
        event: 'tool.failed',
        traceId,
        tool: name,
        error: {
          type: error.constructor.name,
          message: error.message,
          code: error.code
        },
        duration: Date.now() - startTime
      });
      
      throw error;
    }
  }
  
  // Query audit logs
  async queryAuditLog(params) {
    // Only authorized users can query
    if (!params.context.hasRole('auditor')) {
      throw new AuthError('Insufficient privileges to query audit log');
    }
    
    return this.auditLogger.query({
      startTime: params.startTime,
      endTime: params.endTime,
      userId: params.userId,
      event: params.event,
      format: params.format || 'json'
    });
  }
}

// Real audit log entry example
{
  "timestamp": "2025-01-25T10:23:45.123Z",
  "traceId": "550e8400-e29b-41d4-a716-446655440000",
  "event": "tool.called",
  "tool": "update_customer_record",
  "user": "alice@company.com",
  "organization": "comp-123",
  "args": {
    "customerId": "cust-456",
    "fields": ["email", "phone"]
  },
  "permissions": ["customer:write", "pii:access"],
  "ip": "10.0.0.42",
  "sessionId": "sess-789",
  "mcp_server": "enterprise-mcp",
  "mcp_version": "1.2.0"
}

10.5 Audit Trail Explorer

10.5 Audit Trail Explorer

The Zero-Trust Architecture

The Zero-Trust Architecture

By February 2025, the MCP security model had evolved into a complete zero-trust architecture:

By February 2025, the MCP security model had evolved into a complete zero-trust architecture:

MCP Architecture

MCP Architecture

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// Zero-trust MCP architecture
// Community best practice by February 2025

class ZeroTrustMCPServer extends AuditedMCPServer {
  constructor(config) {
    super(config);
    
    this.trustEngine = new TrustEngine({
      // Never trust, always verify
      principles: {
        // 1. Verify explicitly
        authentication: 'required-always',
        tokenValidation: 'every-request',
        
        // 2. Least privilege access
        defaultPermissions: [],
        privilegeEscalation: 'forbidden',
        
        // 3. Assume breach
        monitoring: 'continuous',
        anomalyDetection: true,
        
        // 4. Encrypt everything
        transportSecurity: 'tls-1.3-required',
        dataEncryption: 'at-rest-and-in-transit'
      },
      
      // Dynamic trust scoring
      trustScoring: {
        factors: {
          userReputation: 0.2,
          deviceHealth: 0.2,
          locationContext: 0.1,
          behaviorAnalysis: 0.3,
          timeContext: 0.2
        },
        
        thresholds: {
          high: 0.8,      // Full access
          medium: 0.6,    // Limited access
          low: 0.4,       // Read only
          blocked: 0.0    // No access
        }
      }
    });
  }
  
  async evaluateTrust(context) {
    const factors = {
      // User reputation from past behavior
      userReputation: await this.calculateUserReputation(context.userId),
      
      // Device security posture
      deviceHealth: await this.assessDeviceHealth(context.deviceId),
      
      // Location risk
      locationContext: await this.evaluateLocation(context.ip),
      
      // Behavior anomalies
      behaviorAnalysis: await this.analyzeBehavior(context),
      
      // Time-based risk (off-hours access, etc)
      timeContext: this.evaluateTimeContext(context.timestamp)
    };
    
    // Calculate trust score
    const trustScore = Object.entries(factors).reduce((score, [factor, value]) => {
      return score + (value * this.trustEngine.config.trustScoring.factors[factor]);
    }, 0);
    
    return {
      score: trustScore,
      factors: factors,
      level: this.getTrustLevel(trustScore),
      restrictions: this.getRestrictions(trustScore)
    };
  }
  
  async handleRequest(request, metadata, context) {
    // Evaluate trust for every request
    const trust = await this.evaluateTrust(context);
    
    // Adjust permissions based on trust
    context.permissions = this.adjustPermissions(
      context.permissions,
      trust.level
    );
    
    // Apply restrictions
    if (trust.restrictions.includes('read-only')) {
      if (request.method.includes('write') || request.method.includes('update')) {
        throw new TrustError(
          'Trust level insufficient for write operations',
          { required: 'high', current: trust.level }
        );
      }
    }
    
    // Enhanced monitoring for low trust
    if (trust.level === 'low') {
      this.enhancedMonitoring.track(context, request);
    }
    
    return await super.handleRequest(request, metadata, context);
  }
}

10.6 Trust Score Calculator

10.6 Trust Score Calculator

The Community Security Guidelines

The Community Security Guidelines

By March 2025, the community had distilled months of learning into clear guidelines:

By March 2025, the community had distilled months of learning into clear guidelines:

MCP Security Best Practices

Community-maintained guide

1. Defense in Depth

  • Layer your security (protocol + server + runtime)

  • Assume any layer can fail

  • Monitor everything

2. Principle of Least Privilege

  • Start with no permissions

  • Grant only what's needed

  • Time-bound elevated permissions

3. Zero Trust Always

  • Authenticate every request

  • Validate continuously

  • Trust no one, not even Claude

4. Privacy by Design

  • Minimize data collection

  • Encrypt everything

  • Give users control

5. Transparent Security

  • Show users what MCP can access

  • Log all operations

  • Make security visible

Example 1: Secure File Access

Example 1: Secure File Access

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// ✅ Good: Explicit, limited, audited
{
  permissions: {
    'files:read': {
      paths: ['/project/src'],
      exclude: ['.env', '*.key'],
      audit: true
    }
  }
}

// ❌ Bad: Too broad
{
  permissions: {
    'files:read': {
      paths: ['/']
    }
  }
}

Example 2: Database Access

Example 2: Database Access

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// ✅ Good: Row-level security
async queryDatabase(query, context) {
  // Add row-level security
  const secureQuery = `
    ${query}
    AND organization_id = $1
    AND (visibility = 'public' OR owner_id = $2)
  `;
  
  return await db.query(secureQuery, [
    context.organizationId,
    context.userId
  ]);
}

// ❌ Bad: Direct query execution
async queryDatabase(query) {
  return await db.query(query);
}

10.7 Security Checklist

10.7 Security Checklist

The Security Success Stories

The Security Success Stories

Real organizations shared how MCP security enabled, rather than restricted, their AI adoption:

Real organizations shared how MCP security enabled, rather than restricted, their AI adoption:

Healthcare Provider (February 2025)

"MCP's security model finally let us give doctors AI assistance. Patient data stays encrypted, audit trails satisfy HIPAA, and doctors get help without privacy risks."

Chief Security Officer

Healthcare Provider (February 2025)

"MCP's security model finally let us give doctors AI assistance. Patient data stays encrypted, audit trails satisfy HIPAA, and doctors get help without privacy risks."

Chief Security Officer

Healthcare Provider (February 2025)

"MCP's security model finally let us give doctors AI assistance. Patient data stays encrypted, audit trails satisfy HIPAA, and doctors get help without privacy risks."

Chief Security Officer

Financial Services (March 2025)

"We process millions of transactions daily. MCP's zero-trust architecture and homomorphic encryption let our AI analyze patterns without ever seeing actual account numbers."

VP of Engineering

Financial Services (March 2025)

"We process millions of transactions daily. MCP's zero-trust architecture and homomorphic encryption let our AI analyze patterns without ever seeing actual account numbers."

VP of Engineering

Financial Services (March 2025)

"We process millions of transactions daily. MCP's zero-trust architecture and homomorphic encryption let our AI analyze patterns without ever seeing actual account numbers."

VP of Engineering

Government Agency (March 2025

"The audit capabilities and fine-grained permissions convinced our security team. We can now use AI for document processing while maintaining classification levels."

IT Director

Government Agency (March 2025

"The audit capabilities and fine-grained permissions convinced our security team. We can now use AI for document processing while maintaining classification levels."

IT Director

Government Agency (March 2025

"The audit capabilities and fine-grained permissions convinced our security team. We can now use AI for document processing while maintaining classification levels."

IT Director

The Balance Achieved

The Balance Achieved

The MCP community solved the security paradox not by restricting capabilities, but by making security invisible yet omnipresent:

The MCP community solved the security paradox not by restricting capabilities, but by making security invisible yet omnipresent:

Users get powerful AI assistance

Users get powerful AI assistance

Users get powerful AI assistance

Developers get clear security patterns

Developers get clear security patterns

Developers get clear security patterns

Enterprises get compliance and control

Enterprises get compliance and control

Enterprises get compliance and control

Everyone gets transparency

Everyone gets transparency

Everyone gets transparency

The paradox wasn't solved by choosing between openness and safety. It was solved by achieving both.

The paradox wasn't solved by choosing between openness and safety. It was solved by achieving both.

📜 Audit Logging

🧩 Permissions

🛡️ Sandboxing

🔑 Authentication

📜 Audit Logging

🧩 Permissions

🛡️ Sandboxing

🔑 Authentication

📜 Audit Logging

🧩 Permissions

🛡️ Sandboxing

🔑 Authentication

10.8 Privacy Playground

10.8 Privacy Playground

Your Security Journey

Your Security Journey

As you build MCP servers, security isn't a feature to add later—it's the foundation that enables everything else:

As you build MCP servers, security isn't a feature to add later—it's the foundation that enables everything else:

MCP Server

MCP Server

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// Your secure MCP server starter template
class YourSecureMCPServer extends Server {
  constructor() {
    super({
      name: 'your-secure-server',
      version: '1.0.0'
    });
    
    // Start with security
    this.security = {
      permissions: new PermissionSystem(),
      sandbox: new Sandbox(),
      audit: new AuditLogger(),
      privacy: new PrivacyEngine()
    };
    
    // Build features on secure foundation
    this.features = {
      // Your amazing capabilities here
    };
  }
  
  // Security is not restriction, it's enablement
}

Output

Personalized recommendations

Mentor

AI Analyzes

INPUT

Describe your server

Output

Personalized recommendations

Mentor

AI Analyzes

INPUT

Describe your server

Output

Personalized recommendations

Mentor

AI Analyzes

INPUT

Describe your server

10.9 Security Mento

10.9 Security Mento