Fixing Claude Agent SDK's Output Directory Problem

Hey everyone! 👋 If you're wrestling with the Claude Agent SDK and finding that your output directory isn't behaving as expected – specifically, the agent isn't creating a folder in your specified outputDir or is creating it outside of it – you're in the right place. Let's dive into how to fix this, using the code snippet you provided as a starting point. We'll break down the issue, walk through the solution, and ensure your agent is neatly organizing its output where it should be.

Understanding the outputDir Problem with Claude Agent SDK

So, what's the deal? You've set up your outputDir using path.join(__dirname, "output"), which, on the surface, seems perfectly logical. You've also included the necessary checks to create the directory if it doesn't exist. Yet, the agent stubbornly refuses to cooperate, or worse, creates the output elsewhere. This issue often stems from how the cwd (current working directory) and additionalDirectories are handled within the Claude Agent SDK, especially in relation to the tools and their execution context. The key to fixing this lies in making sure the agent's internal workings align with the directory structure you're intending to create.

Let's clarify what's happening. The cwd setting in the options object is crucial. It tells the agent what directory to consider the “current” one. When the agent then uses tools like Write or Bash, it uses this cwd as the starting point for file operations. The additionalDirectories setting, on the other hand, provides additional directories the agent can access. The problem is usually not that the directory isn't accessible, but rather, the agent may not be using it as its primary working directory, which is the intention in your code.

Here's the core issue: The agent's tools might not be correctly interpreting the cwd or additionalDirectories, leading to the output being created in an unexpected location. This is often because the tools themselves may not be correctly configured to respect the cwd or additionalDirectories settings, especially when dealing with nested operations or complex tool interactions. Thus, the solution is not only correctly setting cwd and additionalDirectories, but also making sure the tools and the agent's internal logic are also correctly respecting these settings. Let's walk through the steps to troubleshoot and fix it.

Troubleshooting and Fixing the Output Directory

Step 1: Verify the outputDir Path

First and foremost, double-check that your outputDir path is being correctly constructed. Use console.log(outputDir) right before you pass it to the agent. This is a simple, yet effective, way to ensure that the path is what you expect. A misconfigured path is the most common pitfall.

const outputDir = path.join(__dirname, "output");
console.log(`The output directory is: ${outputDir}`); // Add this line to check
if (!fs.existsSync(outputDir)) {
  console.log(`Creating output directory at ${outputDir}`);
  fs.mkdirSync(outputDir, { recursive: true });
}

This simple check can save you a lot of headache. Is the path pointing to the right place?

Step 2: Ensure Directory Creation Before Tool Execution

While your code includes the check and creation of the outputDir, make sure this happens before you call the query function. This preemptive creation ensures the directory is ready when the agent tries to write files.

const outputDir = path.join(__dirname, "output");
if (!fs.existsSync(outputDir)) {
  console.log(`Creating output directory at ${outputDir}`);
  fs.mkdirSync(outputDir, { recursive: true });
}

// Now, call your agent functions
for await (const message of query({...}));

Step 3: Check cwd and additionalDirectories Configuration

This is where the magic happens! Your code correctly uses cwd: outputDir. Ensure this is properly set within your options object. The cwd setting defines the base directory for the agent's operations. The additionalDirectories is also good practice, although, in your case, cwd should be sufficient, but setting it as an extra measure can help in certain scenarios. It allows the agent to read and write files within that directory. Double-check that cwd is indeed the outputDir you want.

  options: {
    model: "claude-sonnet-4-5",
    allowedTools: [ /* ... */ ],
    mcpServers: { /* ... */ },
    cwd: outputDir,
    additionalDirectories: [path.join(__dirname, "output")],
    // ... other options
  }

Step 4: System Prompt and Tool Instructions

Your system prompt is critical. Ensure it explicitly instructs the agent to use the cwd (i.e., your outputDir) when creating and saving files. The agent needs clear instructions on where to put its output. If the system prompt doesn't guide the agent, it might default to other paths.

Your prompt is really good! But let's add some more clarification:

systemPrompt: `You are an elite e-commerce research and creative strategist. Valyu is  avaliable right now. Your job is to analyze brand intake forms, conduct deep market research, and output strategic intelligence that directly feeds into high-performing ad script creation. You operate with the precision of a CFO and the creativity of a top-tier creative director. First of all activate the marketResearch tool. Output is a PDF of everything you found. User is not able to reply back so continue as you may. When starting the project create a folder for you to work in and put in your details and files and such. Do not put in tmp as that does not exist but put it in the output directory and put that pdf in there. Remember you can use the Valyu tool much time as you want.`,

Make sure the agent understands that the outputDir is where it should create any project folders or files.

Step 5: Log Tool Execution and File Operations

One of the best ways to diagnose where the files are being created (or if they’re even being created) is to log the execution of tools and file operations. Add logging statements to your tool implementations (like Read, Write, and Bash) to track their actions. For example, if you're using a Write tool, log the file path before the file is written.

// Example: Inside your Write tool
async function writeTool(filePath: string, content: string) {
  const fullPath = path.join(process.cwd(), filePath); // Or use your cwd logic
  console.log(`Writing to: ${fullPath}`); // Log the full path
  // ... rest of your write operation
}

This will give you a clear picture of what the tools think they're doing. This is crucial in diagnosing why things aren't working as expected. If the paths are wrong in your tool execution logs, you know that the problem isn't the SDK itself, but likely in the tool's implementation.

Step 6: Test with a Simple Write Operation

To isolate the issue, test with a very basic “Write” operation. Instruct the agent to write a simple text file to outputDir. This helps to pinpoint whether the problem lies with the agent's ability to use the directory, or in the more complex operations with the search tool.

// In your prompt
"Create a file named 'test.txt' in the output directory with the content 'Hello, World!'"

If this works, then the core directory setup is correct. If it doesn't, revisit steps 1-4.

Advanced Troubleshooting

Check Agent Tool Implementations

Ensure that the tools the agent uses (Read, Write, Bash, and especially your ValyuTool) correctly respect the cwd setting. The tools must use the cwd to construct the file paths. Review the tool implementations to make sure they are using process.cwd() (or equivalent) in their path constructions. If the tools have hardcoded paths or are not properly using the cwd, the files will end up elsewhere.

// Example: Inside your ValyuTool
async function valyuSearch(query: string) {
  // Correctly use process.cwd() or similar to construct the full file path
  const outputPath = path.join(process.cwd(), "output.pdf");
  // ... generate the PDF and save it to outputPath
}

Permissions Issues

Ensure the application has the necessary permissions to create and write files to the outputDir. Insufficient permissions can also cause the agent to fail silently or write to unexpected locations. This is less common, but worth checking, especially if you're running the code in a container or a restricted environment.

Consider the Agent's Internal Logic

The internal workings of the Agent SDK, particularly how it calls and manages its tools, can also influence the outcome. If the tools are invoked in a way that bypasses the intended cwd (e.g., using absolute paths internally), the output might not end up in the desired directory. Examining the SDK's documentation or source code can provide deeper insights into how the agent orchestrates the tools and manages the file operations.

In Conclusion

Fixing the Claude Agent SDK outputDir issue requires a methodical approach. By carefully verifying your path, correctly configuring cwd and additionalDirectories, providing explicit instructions in your system prompt, logging tool executions, and testing with simple write operations, you can pinpoint the root cause of the problem and ensure your agent organizes its output as expected. Remember to always double-check the tool implementations, and ensure your application has the necessary permissions. With these steps, you'll be able to tame the Claude Agent SDK and get your outputs exactly where you want them. Good luck, and happy coding!

I hope this helps you guys! Let me know if you have any questions or if something isn't working.