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Claude Agent SDK - Structured Outputs & Error Prevention Guide

Package : @anthropic-ai/claude-agent-sdk@0.2.12 Breaking Changes : v0.1.45 - Structured outputs (Nov 2025), v0.1.0 - No default system prompt, settingSources required

What's New in v0.1.45+ (Nov 2025)

Major Features:

1. Structured Outputs (v0.1.45, Nov 14, 2025)

• JSON schema validation - Guarantees responses match exact schemas
• outputFormat parameter - Define output structure with JSON schema or Zod
• Access validated results - Via message.structured_output
• Beta header required : structured-outputs-2025-11-13
• Type safety - Full TypeScript inference with Zod schemas

Example:

import { query } from "@anthropic-ai/claude-agent-sdk";
import { z } from "zod";
import { zodToJsonSchema } from "zod-to-json-schema";

const schema = z.object({
  summary: z.string(),
  sentiment: z.enum(['positive', 'neutral', 'negative']),
  confidence: z.number().min(0).max(1)
});

const response = query({
  prompt: "Analyze this code review feedback",
  options: {
    model: "claude-sonnet-4-5",
    outputFormat: {
      type: "json_schema",
      json_schema: {
        name: "AnalysisResult",
        strict: true,
        schema: zodToJsonSchema(schema)
      }
    }
  }
});

for await (const message of response) {
  if (message.type === 'result' && message.structured_output) {
    // Guaranteed to match schema
    const validated = schema.parse(message.structured_output);
    console.log(`Sentiment: ${validated.sentiment}`);
  }
}

Zod Compatibility (v0.1.71+): SDK supports both Zod v3.24.1+ and Zod v4.0.0+ as peer dependencies. Import remains import { z } from "zod" for either version.

2. Plugins System (v0.1.27)

• plugins array - Load local plugin paths
• Custom plugin support - Extend agent capabilities

3. Hooks System (v0.1.0+)

All 12 Hook Events:

Hook Configuration:

const response = query({
  prompt: "...",
  options: {
    hooks: {
      PreToolUse: async (input) => {
        console.log(`Tool: ${input.toolName}`);
        return { allow: true };  // or { allow: false, message: "..." }
      },
      PostToolUse: async (input) => {
        await logToolUsage(input.toolName, input.result);
      }
    }
  }
});

4. Additional Options

• fallbackModel - Automatic model fallback on failures
• maxThinkingTokens - Control extended thinking budget
• strictMcpConfig - Strict MCP configuration validation
• continue - Resume with new prompt (differs from resume)
• permissionMode: 'plan' - New permission mode for planning workflows

📚 Docs : https://platform.claude.com/docs/en/agent-sdk/structured-outputs

The Complete Claude Agent SDK Reference

Table of Contents

1. Core Query API
2. Tool Integration
3. MCP Servers
4. Subagent Orchestration
5. Session Management
6. Permission Control
7. Sandbox Settings
8. File Checkpointing
9. Filesystem Settings
10. Query Object Methods
11. Message Types & Streaming
12. Error Handling
13. Known Issues

Core Query API

Key signature:

query(prompt: string | AsyncIterable<SDKUserMessage>, options?: Options)
  -> AsyncGenerator<SDKMessage>

Critical Options:

• outputFormat - Structured JSON schema validation (v0.1.45+)
• settingSources - Filesystem settings loading ('user'|'project'|'local')
• canUseTool - Custom permission logic callback
• agents - Programmatic subagent definitions
• mcpServers - MCP server configuration
• permissionMode - 'default'|'acceptEdits'|'bypassPermissions'|'plan'
• betas - Enable beta features (e.g., 1M context window)
• sandbox - Sandbox settings for secure execution
• enableFileCheckpointing - Enable file state snapshots

Extended Context (1M Tokens)

Enable 1 million token context window:

const response = query({
  prompt: "Analyze this large codebase",
  options: {
    betas: ['context-1m-2025-08-07'],  // Enable 1M context
    model: "claude-sonnet-4-5"
  }
});

System Prompt Configuration

Two forms of systemPrompt:

// 1. Simple string
systemPrompt: "You are a helpful coding assistant."

// 2. Preset with optional append (preserves Claude Code defaults)
systemPrompt: {
  type: 'preset',
  preset: 'claude_code',
  append: "\n\nAdditional context: Focus on security."
}

Use preset form when you want Claude Code's default behaviors plus custom additions.

Tool Integration (Built-in + Custom)

Tool Control:

• allowedTools - Whitelist (takes precedence)
• disallowedTools - Blacklist
• canUseTool - Custom permission callback (see Permission Control section)

Built-in Tools: Read, Write, Edit, Bash, Grep, Glob, WebSearch, WebFetch, Task, NotebookEdit, BashOutput, KillBash, ListMcpResources, ReadMcpResource, AskUserQuestion

AskUserQuestion Tool (v0.1.71+)

Enable user interaction during agent execution:

const response = query({
  prompt: "Review and refactor the codebase",
  options: {
    allowedTools: ["Read", "Write", "Edit", "AskUserQuestion"]
  }
});

// Agent can now ask clarifying questions
// Questions appear in message stream as tool_call with name "AskUserQuestion"

Use cases:

• Clarify ambiguous requirements mid-task
• Get user approval before destructive operations
• Present options and get selection

Tools Configuration (v0.1.57+)

Three forms of tool configuration:

// 1. Exact allowlist (string array)
tools: ["Read", "Write", "Grep"]

// 2. Disable all tools (empty array)
tools: []

// 3. Preset with defaults (object form)
tools: { type: 'preset', preset: 'claude_code' }

Note: allowedTools and disallowedTools still work but tools provides more flexibility.

MCP Servers (Model Context Protocol)

Server Types:

• In-process - createSdkMcpServer() with tool() definitions
• External - stdio, HTTP, SSE transport

Tool Definition:

tool(name: string, description: string, zodSchema, handler)

Handler Return:

{ content: [{ type: "text", text: "..." }], isError?: boolean }

External MCP Servers (stdio)

const response = query({
  prompt: "List files and analyze Git history",
  options: {
    mcpServers: {
      // Filesystem server
      "filesystem": {
        command: "npx",
        args: ["@modelcontextprotocol/server-filesystem"],
        env: {
          ALLOWED_PATHS: "/Users/developer/projects:/tmp"
        }
      },
      // Git operations server
      "git": {
        command: "npx",
        args: ["@modelcontextprotocol/server-git"],
        env: {
          GIT_REPO_PATH: "/Users/developer/projects/my-repo"
        }
      }
    },
    allowedTools: [
      "mcp__filesystem__list_files",
      "mcp__filesystem__read_file",
      "mcp__git__log",
      "mcp__git__diff"
    ]
  }
});

External MCP Servers (HTTP/SSE)

const response = query({
  prompt: "Analyze data from remote service",
  options: {
    mcpServers: {
      "remote-service": {
        url: "https://api.example.com/mcp",
        headers: {
          "Authorization": "Bearer your-token-here",
          "Content-Type": "application/json"
        }
      }
    },
    allowedTools: ["mcp__remote-service__analyze"]
  }
});

MCP Tool Naming Convention

Format : mcp__<server-name>__<tool-name>

CRITICAL:

• Server name and tool name MUST match configuration
• Use double underscores (__) as separators
• Include in allowedTools array

Examples: mcp__weather-service__get_weather, mcp__filesystem__read_file

Subagent Orchestration

AgentDefinition Type

type AgentDefinition = {
  description: string;        // When to use this agent
  prompt: string;             // System prompt for agent
  tools?: string[];           // Allowed tools (optional)
  model?: 'sonnet' | 'opus' | 'haiku' | 'inherit';  // Model (optional)
  skills?: string[];          // Skills to load (v0.2.10+)
  maxTurns?: number;          // Maximum turns before stopping (v0.2.10+)
}

Field Details:

• description : When to use agent (used by main agent for delegation)
• prompt : System prompt (defines role, inherits main context)
• tools : Allowed tools (if omitted, inherits from main agent)
• model : Model override (haiku/sonnet/opus/inherit)
• skills : Skills to load for agent (v0.2.10+)
• maxTurns : Limit agent to N turns before returning control (v0.2.10+)

Usage:

agents: {
  "security-checker": {
    description: "Security audits and vulnerability scanning",
    prompt: "You check security. Scan for secrets, verify OWASP compliance.",
    tools: ["Read", "Grep", "Bash"],
    model: "sonnet",
    skills: ["security-best-practices"],  // Load specific skills
    maxTurns: 10  // Limit to 10 turns
  }
}

⚠️ Subagent Cleanup Warning

Known Issue : Subagents don't stop when parent agent stops (Issue #132)

When a parent agent is stopped (via cancellation or error), spawned subagents continue running as orphaned processes. This can lead to:

• Resource leaks
• Continued tool execution after parent stopped
• RAM out-of-memory in recursive scenarios (Claude Code Issue #4850)

Workaround : Implement cleanup in Stop hooks:

const response = query({
  prompt: "Deploy to production",
  options: {
    agents: {
      "deployer": {
        description: "Handle deployments",
        prompt: "Deploy the application",
        tools: ["Bash"]
      }
    },
    hooks: {
      Stop: async (input) => {
        // Manual cleanup of spawned processes
        console.log("Parent stopped - cleaning up subagents");
        // Implement process tracking and termination
      }
    }
  }
});

Enhancement Tracking : Issue #142 proposes auto-termination

Session Management

Options:

• resume: sessionId - Continue previous session
• forkSession: true - Create new branch from session
• continue: prompt - Resume with new prompt (differs from resume)

Session Forking Pattern (Unique Capability):

// Explore alternative without modifying original
const forked = query({
  prompt: "Try GraphQL instead of REST",
  options: {
    resume: sessionId,
    forkSession: true  // Creates new branch, original session unchanged
  }
});

Capture Session ID:

for await (const message of response) {
  if (message.type === 'system' && message.subtype === 'init') {
    sessionId = message.session_id;  // Save for later resume/fork
  }
}

V2 Session APIs (Preview - v0.1.54+)

Simpler multi-turn conversation pattern:

import {
  unstable_v2_createSession,
  unstable_v2_resumeSession,
  unstable_v2_prompt
} from "@anthropic-ai/claude-agent-sdk";

// Create a new session
const session = await unstable_v2_createSession({
  model: "claude-sonnet-4-5",
  workingDirectory: process.cwd(),
  allowedTools: ["Read", "Grep", "Glob"]
});

// Send prompts and stream responses
const stream = unstable_v2_prompt(session, "Analyze the codebase structure");
for await (const message of stream) {
  console.log(message);
}

// Continue conversation in same session
const stream2 = unstable_v2_prompt(session, "Now suggest improvements");
for await (const message of stream2) {
  console.log(message);
}

// Resume a previous session
const resumedSession = await unstable_v2_resumeSession(session.sessionId);

Note: V2 APIs are in preview (unstable_ prefix). The .receive() method was renamed to .stream() in v0.1.72.

Permission Control

Permission Modes:

type PermissionMode = "default" | "acceptEdits" | "bypassPermissions" | "plan";

• default - Standard permission checks
• acceptEdits - Auto-approve file edits
• bypassPermissions - Skip ALL checks (use in CI/CD only)
• plan - Planning mode (v0.1.45+)

Custom Permission Logic

const response = query({
  prompt: "Deploy application to production",
  options: {
    permissionMode: "default",
    canUseTool: async (toolName, input) => {
      // Allow read-only operations
      if (['Read', 'Grep', 'Glob'].includes(toolName)) {
        return { behavior: "allow" };
      }

      // Deny destructive bash commands
      if (toolName === 'Bash') {
        const dangerous = ['rm -rf', 'dd if=', 'mkfs', '> /dev/'];
        if (dangerous.some(pattern => input.command.includes(pattern))) {
          return {
            behavior: "deny",
            message: "Destructive command blocked for safety"
          };
        }
      }

      // Require confirmation for deployments
      if (input.command?.includes('deploy') || input.command?.includes('kubectl apply')) {
        return {
          behavior: "ask",
          message: "Confirm deployment to production?"
        };
      }

      // Allow by default
      return { behavior: "allow" };
    }
  }
});

canUseTool Callback

type CanUseToolCallback = (
  toolName: string,
  input: any
) => Promise<PermissionDecision>;

type PermissionDecision =
  | { behavior: "allow" }
  | { behavior: "deny"; message?: string }
  | { behavior: "ask"; message?: string };

Examples:

// Block all file writes
canUseTool: async (toolName, input) => {
  if (toolName === 'Write' || toolName === 'Edit') {
    return { behavior: "deny", message: "No file modifications allowed" };
  }
  return { behavior: "allow" };
}

// Require confirmation for specific files
canUseTool: async (toolName, input) => {
  const sensitivePaths = ['/etc/', '/root/', '.env', 'credentials.json'];
  if ((toolName === 'Write' || toolName === 'Edit') &&
      sensitivePaths.some(path => input.file_path?.includes(path))) {
    return {
      behavior: "ask",
      message: `Modify sensitive file ${input.file_path}?`
    };
  }
  return { behavior: "allow" };
}

// Log all tool usage
canUseTool: async (toolName, input) => {
  console.log(`Tool requested: ${toolName}`, input);
  await logToDatabase(toolName, input);
  return { behavior: "allow" };
}

Sandbox Settings (Security-Critical)

Enable sandboxed execution for Bash commands:

const response = query({
  prompt: "Run system diagnostics",
  options: {
    sandbox: {
      enabled: true,
      autoAllowBashIfSandboxed: true,  // Auto-approve bash in sandbox
      excludedCommands: ["rm", "dd", "mkfs"],  // Never auto-approve these
      allowUnsandboxedCommands: false  // Deny unsandboxable commands
    }
  }
});

SandboxSettings Type

type SandboxSettings = {
  enabled: boolean;
  autoAllowBashIfSandboxed?: boolean;  // Default: false
  excludedCommands?: string[];
  allowUnsandboxedCommands?: boolean;  // Default: false
  network?: NetworkSandboxSettings;
  ignoreViolations?: SandboxIgnoreViolations;
};

type NetworkSandboxSettings = {
  enabled: boolean;
  proxyUrl?: string;  // HTTP proxy for network requests
};

Key Options:

• enabled - Activate sandbox isolation
• autoAllowBashIfSandboxed - Skip permission prompts for safe bash commands
• excludedCommands - Commands that always require permission
• allowUnsandboxedCommands - Allow commands that can't be sandboxed (risky)
• network.proxyUrl - Route network through proxy for monitoring

Best Practice: Always use sandbox in production agents handling untrusted input.

File Checkpointing

Enable file state snapshots for rollback capability:

const response = query({
  prompt: "Refactor the authentication module",
  options: {
    enableFileCheckpointing: true  // Enable file snapshots
  }
});

// Later: rewind file changes to a specific point
for await (const message of response) {
  if (message.type === 'user' && message.uuid) {
    // Can rewind to this point later
    const userMessageUuid = message.uuid;

    // To rewind (call on Query object)
    await response.rewindFiles(userMessageUuid);
  }
}

Use cases:

• Undo failed refactoring attempts
• A/B test code changes
• Safe exploration of alternatives

Filesystem Settings

Setting Sources:

type SettingSource = 'user' | 'project' | 'local';

• user - ~/.claude/settings.json (global)
• project - .claude/settings.json (team-shared)
• local - .claude/settings.local.json (gitignored overrides)

Default: NO settings loaded (settingSources: [])

Settings Priority

When multiple sources loaded, settings merge in this order (highest priority first):

1. Programmatic options (passed to query()) - Always win
2. Local settings (.claude/settings.local.json)
3. Project settings (.claude/settings.json)
4. User settings (~/.claude/settings.json)

Example:

// .claude/settings.json
{
  "allowedTools": ["Read", "Write", "Edit"]
}

// .claude/settings.local.json
{
  "allowedTools": ["Read"]  // Overrides project settings
}

// Programmatic
const response = query({
  options: {
    settingSources: ["project", "local"],
    allowedTools: ["Read", "Grep"]  // ← This wins
  }
});

// Actual allowedTools: ["Read", "Grep"]

Best Practice: Use settingSources: ["project"] in CI/CD for consistent behavior.

Query Object Methods

The query() function returns a Query object with these methods:

const q = query({ prompt: "..." });

// Async iteration (primary usage)
for await (const message of q) { ... }

// Runtime model control
await q.setModel("claude-opus-4-5");           // Change model mid-session
await q.setMaxThinkingTokens(4096);            // Set thinking budget

// Introspection
const models = await q.supportedModels();     // List available models
const commands = await q.supportedCommands(); // List available commands
const account = await q.accountInfo();        // Get account details

// MCP status
const status = await q.mcpServerStatus();     // Check MCP server status
// Returns: { [serverName]: { status: 'connected' | 'failed', error?: string } }

// File operations (requires enableFileCheckpointing)
await q.rewindFiles(userMessageUuid);         // Rewind to checkpoint

Use cases:

• Dynamic model switching based on task complexity
• Monitoring MCP server health
• Adjusting thinking budget for reasoning tasks

Message Types & Streaming

Message Types:

• system - Session init/completion (includes session_id)
• assistant - Agent responses
• tool_call - Tool execution requests
• tool_result - Tool execution results
• error - Error messages
• result - Final result (includes structured_output for v0.1.45+)

Streaming Pattern:

for await (const message of response) {
  if (message.type === 'system' && message.subtype === 'init') {
    sessionId = message.session_id;  // Capture for resume/fork
  }
  if (message.type === 'result' && message.structured_output) {
    // Structured output available (v0.1.45+)
    const validated = schema.parse(message.structured_output);
  }
}

Error Handling

Error Codes:

Known Issues Prevention

This skill prevents 14 documented issues:

Issue #1: CLI Not Found Error

Error : "Claude Code CLI not installed" Source : SDK requires Claude Code CLI Why It Happens : CLI not installed globally Prevention : Install before using SDK: npm install -g @anthropic-ai/claude-code

Issue #2: Authentication Failed

Error : "Invalid API key" Source : Missing or incorrect ANTHROPIC_API_KEY Why It Happens : Environment variable not set Prevention : Always set export ANTHROPIC_API_KEY="sk-ant-..."

Issue #3: Permission Denied Errors

Error : Tool execution blocked Source : permissionMode restrictions Why It Happens : Tool not allowed by permissions Prevention : Use allowedTools or custom canUseTool callback

Issue #4: Context Length Exceeded (Session-Breaking)

Error : "Prompt too long" Source : Input exceeds model context window (Issue #138) Why It Happens : Large codebase, long conversations

⚠️ Critical Behavior : Once a session hits context limit:

1. All subsequent requests to that session return "Prompt too long"
2. /compact command fails with same error
3. Session is permanently broken and must be abandoned

Prevention Strategies :

// 1. Proactive session forking (create checkpoints before hitting limit)
const checkpoint = query({
  prompt: "Checkpoint current state",
  options: {
    resume: sessionId,
    forkSession: true  // Create branch before hitting limit
  }
});

// 2. Monitor time and rotate sessions proactively
const MAX_SESSION_TIME = 80 * 60 * 1000;  // 80 minutes (before 90-min crash)
let sessionStartTime = Date.now();

function shouldRotateSession() {
  return Date.now() - sessionStartTime > MAX_SESSION_TIME;
}

// 3. Start new sessions before hitting context limits
if (shouldRotateSession()) {
  const summary = await getSummary(currentSession);
  const newSession = query({
    prompt: `Continue with context: ${summary}`
  });
  sessionStartTime = Date.now();
}

Note : SDK auto-compacts, but if limit is reached, session becomes unrecoverable

Issue #5: Tool Execution Timeout

Error : Tool doesn't respond Source : Long-running tool execution Why It Happens : Tool takes too long (>5 minutes default) Prevention : Implement timeout handling in tool implementations

Issue #6: Session Not Found

Error : "Invalid session ID" Source : Session expired or invalid Why It Happens : Session ID incorrect or too old Prevention : Capture session_id from system init message

Issue #7: MCP Server Connection Failed

Error : Server not responding Source : Server not running or misconfigured Why It Happens : Command/URL incorrect, server crashed Prevention : Test MCP server independently, verify command/URL

Issue #8: Subagent Definition Errors

Error : Invalid AgentDefinition Source : Missing required fields Why It Happens : description or prompt missing Prevention : Always include description and prompt fields

Issue #9: Settings File Not Found

Error : "Cannot read settings" Source : Settings file doesn't exist Why It Happens : settingSources includes non-existent file Prevention : Check file exists before including in sources

Issue #10: Tool Name Collision

Error : Duplicate tool name Source : Multiple tools with same name Why It Happens : Two MCP servers define same tool name Prevention : Use unique tool names, prefix with server name

Issue #11: Zod Schema Validation Error

Error : Invalid tool input Source : Input doesn't match Zod schema Why It Happens : Agent provided wrong data type Prevention : Use descriptive Zod schemas with .describe()

Issue #12: Filesystem Permission Denied

Error : Cannot access path Source : Restricted filesystem access Why It Happens : Path outside workingDirectory or no permissions Prevention : Set correct workingDirectory, check file permissions

Issue #13: MCP Server Config Missing type Field

Error : "Claude Code process exited with code 1" (cryptic, no context) Source : GitHub Issue #131 Why It Happens : URL-based MCP servers require explicit type: "http" or type: "sse" field Prevention : Always specify transport type for URL-based MCP servers

// ❌ Wrong - missing type field (causes cryptic exit code 1)
mcpServers: {
  "my-server": {
    url: "https://api.example.com/mcp"
  }
}

// ✅ Correct - type field required for URL-based servers
mcpServers: {
  "my-server": {
    url: "https://api.example.com/mcp",
    type: "http"  // or "sse" for Server-Sent Events
  }
}

Diagnostic Clue : If you see "process exited with code 1" with no other context, check your MCP server configuration for missing type fields.

Issue #14: MCP Tool Result with Unicode Line Separators

Error : JSON parse error, agent hangs Source : GitHub Issue #137 Why It Happens : Unicode U+2028 (line separator) and U+2029 (paragraph separator) are valid in JSON but break JavaScript parsing Prevention : Escape these characters in MCP tool results

// MCP tool handler - sanitize external data
tool("fetch_content", "Fetch text content", {}, async (args) => {
  const content = await fetchExternalData();

  // ✅ Sanitize Unicode line/paragraph separators
  const sanitized = content
    .replace(/\u2028/g, '\\u2028')
    .replace(/\u2029/g, '\\u2029');

  return {
    content: [{ type: "text", text: sanitized }]
  };
});

When This Matters : External data sources (APIs, web scraping, user input) that may contain these characters

Related : MCP Python SDK Issue #1356

Official Documentation

• Agent SDK Overview : https://platform.claude.com/docs/en/api/agent-sdk/overview
• TypeScript API : https://platform.claude.com/docs/en/api/agent-sdk/typescript
• Structured Outputs : https://platform.claude.com/docs/en/agent-sdk/structured-outputs
• GitHub (TypeScript) : https://github.com/anthropics/claude-agent-sdk-typescript
• CHANGELOG : https://github.com/anthropics/claude-agent-sdk-typescript/blob/main/CHANGELOG.md

Token Efficiency :

• Without skill : ~15,000 tokens (MCP setup, permission patterns, session APIs, sandbox config, hooks, structured outputs, error handling)
• With skill : ~4,500 tokens (comprehensive v0.2.12 coverage + error prevention + advanced patterns)
• Savings : ~70% (~10,500 tokens)

Errors prevented : 14 documented issues with exact solutions (including 2 community-sourced gotchas) Key value : V2 Session APIs, Sandbox Settings, File Checkpointing, Query methods, AskUserQuestion tool, structured outputs (v0.1.45+), session forking, canUseTool patterns, complete hooks system (12 events), Zod v4 support, subagent cleanup patterns

Last verified : 2026-01-20 | Skill version : 3.1.0 | Changes : Added Issue #13 (MCP type field), Issue #14 (Unicode U+2028/U+2029), expanded Issue #4 (session-breaking), added subagent cleanup warning with Stop hook pattern

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