[Bug]: Code implementation failed: File tree structure not found, please run file tree creation first

[jackhawa]

Do you need to file an issue?

• [x] I have searched the existing issues and this bug is not already filed.
• [ ] I believe this is a legitimate bug, not just a question or feature request.

Describe the bug

I have processed a arxiv paper in pdf format and all stages have passed except the Code implementation.

🔄 Workflow Stages Completed 📄 Document Processing: ✅ 🔍 Reference Analysis: ✅ 📋 Plan Generation: ✅ 📦 Repository Download: ✅ 🗂️ Codebase Indexing: ✅ ⚙️ Code Implementation: ⚠️

The error I got: Code implementation failed: File tree structure not found, please run file tree creation first

I have used openai gpt-5 model (medium reasoning effort) with brave search enabled. I have provided both open ai key and brave key. I have also installed all dependencies correctly.

Attached is the paper I have used to import.

MCTR.pdf

Can you assist me in understanding and fixing this issue?

Steps to reproduce

No response

Expected Behavior

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DeepCode Config Used

Paste your config here

Logs and screenshots

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Additional Information

• DeepCode Version:
• Operating System:
• Python Version:
• Related Issues:

[jackhawa]

After some debugging, I have seen this message in the log (when setting level to debug)

{
  "data": {
    "id": "chatcmpl-CBvYO4cGGkkzdPPLphDrbN1jAc6W1",
    "choices": [
      {
        "finish_reason": "stop",
        "index": 0,
        "logprobs": null,
        "message": {
          "content": "I looked through the implementation plan you provided but I couldn't find any \"Code Organization\" or \"File Tree\" section or any explicit 
file tree to extract. I need the exact file tree listed in the plan to generate the required mkdir/touch commands and run them.\n\nPlease either:\n- Paste the \"Code 
Organization\" / \"File Tree\" section (the exact paths and files), or\n- Confirm that you want me to create a default skeleton (I can propose one such as a Python 
package with src/, tests/, README.md, etc.—I will show the exact tree first and then create it if you approve).\n\nWhich would you like?",
          "refusal": null,
          "role": "assistant",
          "annotations": [],
          "audio": null,
          "function_call": null,
          "tool_calls": null
        }
      }
    ],
    "created": 1756958880,
    "model": "gpt-5-mini-2025-08-07",
    "object": "chat.completion",
    "service_tier": "default",
    "system_fingerprint": null,
    "usage": {
      "completion_tokens": 394,
      "prompt_tokens": 781,
      "total_tokens": 1175,
      "completion_tokens_details": {
        "accepted_prediction_tokens": "0",
        "audio_tokens": "0",
        "reasoning_tokens": 256,
        "rejected_prediction_tokens": "0"
      },
      "prompt_tokens_details": {
        "audio_tokens": "0",
        "cached_tokens": "0"
      }
    },
    "_request_id": "req_a3409c72484947fea1944118cef2b6bd"
  }
}

Looks like the agent is trying to ask a question but I have never gotten a chance to respond to it. Is there a way to do that? Thanks.

[jackhawa]

I have added an extra statement in the STRUCTURE_GENERATOR_PROMPT towards the end and it worked.

If you could not find any Code Organization or File Tree section or any explicit file tree to extract, create a default skeleton structure based on common practices for the project type mentioned in the plan.

[matr1xp]

I get the same issue when using the Web interface. Running on cli it works fine.

[osiloke]

Same here, i'll try the cli

[jackhawa]

Thanks @matr1xp 👍

[eskrodelis]

Same here will try cli.

[Zongwei9888]

The problem has been solved, you can update the new version of DeepCode! Thank you!