[Bug]: Just stops on one error during code implementation stage.

### Do you need to file an issue?

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

### Describe the bug

I cloned the git repo and started using it with web interface. Several times I have tried using it with diffrent models but along the way everytime I got this following json output error and deepcode stopped without finishing its job. 
Error: {
"analysis_result":"Integrated into complete workflow"
"download_result":"Integrated into complete workflow"
"repo_result":"Chat-based planning and implementation pipeline completed for /Users/okyozcan/Downloads/deepcode/DeepCode/deepcode_lab/papers/chat_project_1757004202
❌ Code implementation failed: Unterminated string starting at: line 1 column 25 (char 24)"
"status":"success"
}

### Steps to reproduce

Download the source using git clone.
Setup project.
Run using "uv"
Use web interface with openrouter endpoint and key.

### Expected Behavior

Finishing the workflow with no errors.

### DeepCode Config Used

$schema: ./schema/mcp-agent.config.schema.json

# Default search server configuration
# Options: "brave" or "bocha-mcp"
default_search_server: "brave"

# Planning mode configuration
# Options: "segmented" or "traditional"
# segmented: Breaks down large tasks to avoid token truncation (recommended)
# traditional: Uses parallel agents but may hit token limits
planning_mode: "segmented"

# Document segmentation configuration
document_segmentation:
  enabled: true  # Whether to use intelligent document segmentation
  size_threshold_chars: 50000  # Document size threshold (in characters) to trigger segmentation
  # If document size > threshold and enabled=true, use segmentation workflow
  # If document size <= threshold or enabled=false, use traditional full-document reading

execution_engine: asyncio
logger:
  transports: [console, file]
  level: info
  progress_display: true
  path_settings:
    path_pattern: "logs/mcp-agent-{unique_id}.jsonl"
    unique_id: "timestamp" # Options: "timestamp" or "session_id"
    timestamp_format: "%Y%m%d_%H%M%S"



mcp:
  servers:
    brave:
      # On windows replace the command and args line to use `node` and the absolute path to the server.
      # Use `npm i -g @modelcontextprotocol/server-brave-search` to install the server globally.
      # Use `npm -g root` to find the global node_modules path.`
      # command: "node"
      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-brave-search/dist/index.js"]
      command: "npx"
      args: ["-y", "@modelcontextprotocol/server-brave-search"]
      env:
        # You can also place your BRAVE_API_KEY in the fastagent.secrets.yaml file.
        BRAVE_API_KEY: ""
    filesystem:
      # On windows update the command and arguments to use `node` and the absolute path to the server.
      # Use `npm i -g @modelcontextprotocol/server-filesystem` to install the server globally.
      # Use `npm -g root` to find the global node_modules path.`
      # command: "node"
      # args: ["c:/Program Files/nodejs/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js","."]
      command: "npx"
      args: ["-y", "@modelcontextprotocol/server-filesystem"]
    fetch:
      command: "uvx"
      args: ["mcp-server-fetch"]
    github-downloader:
      command: "python"
      args: ["tools/git_command.py"]
      env:
        PYTHONPATH: "."
    file-downloader:
      command: "python"
      args: ["tools/pdf_downloader.py"]
      env:
        PYTHONPATH: "."
    command-executor:
      command: "python"
      args: ["tools/command_executor.py"]
      env:
        PYTHONPATH: "."
    code-implementation:
      command: "python"
      args: ["tools/code_implementation_server.py"]
      env:
        PYTHONPATH: "."
      description: "Paper code reproduction tool server - provides file operations, code execution, search and other functions"
    code-reference-indexer:
      command: "python"
      args: ["tools/code_reference_indexer.py"]
      env:
        PYTHONPATH: "."
      description: "Code reference indexer server - Provides intelligent code reference search from indexed repositories"
    bocha-mcp:
      command: "python3"
      args: ["tools/bocha_search_server.py"]
      env:
        PYTHONPATH: "."
        BOCHA_API_KEY: ""
    document-segmentation:
      command: "python"
      args: ["tools/document_segmentation_server.py"]
      env:
        PYTHONPATH: "."
      description: "Document segmentation server - Provides intelligent document analysis and segmented reading to optimize token usage"

openai:
  # Secrets (API keys, etc.) are stored in an mcp_agent.secrets.yaml file which can be gitignored
  #  default_model: "o3-mini"
  default_model: "openai/gpt-5"


anthropic:


### Logs and screenshots

{"level":"INFO","timestamp":"2025-09-04T19:42:28.206169","namespace":"mcp_agent.core.context","message":"Configuring logger with level: info"}
{"level":"INFO","timestamp":"2025-09-04T19:42:28.208857","namespace":"mcp_agent.paper_to_code","message":"Loading subagents from configuration..."}
{"level":"INFO","timestamp":"2025-09-04T19:42:28.209509","namespace":"mcp_agent.paper_to_code","message":"MCPApp initialized","data":{"data":{"progress_action":"Running","target":"paper_to_code","agent_name":"mcp_application_loop","session_id":"c1082376-75e8-4a16-9793-cfd3793e1bd3"}}}
{"level":"INFO","timestamp":"2025-09-04T19:42:29.153164","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"brave: Up and running with a persistent connection!"}
{"level":"INFO","timestamp":"2025-09-04T19:43:21.637288","namespace":"mcp_agent.mcp.mcp_aggregator.ChatPlanningAgent","message":"Last aggregator closing, shutting down all persistent connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:43:21.637401","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"Disconnecting all persistent server connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:43:21.637873","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"brave: Requesting shutdown..."}
{"level":"INFO","timestamp":"2025-09-04T19:43:21.842278","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"All persistent server connections signaled to disconnect."}
{"level":"INFO","timestamp":"2025-09-04T19:43:21.842583","namespace":"mcp_agent.mcp.mcp_aggregator.ChatPlanningAgent","message":"Connection manager successfully closed and removed from context"}
{"level":"INFO","timestamp":"2025-09-04T19:43:36.134809","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"command-executor: Up and running with a persistent connection!"}
{"level":"INFO","timestamp":"2025-09-04T19:43:57.529164","namespace":"mcp_agent.mcp.mcp_aggregator.StructureGeneratorAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"execute_commands","server_name":"command-executor","agent_name":"StructureGeneratorAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:44:07.615317","namespace":"mcp_agent.mcp.mcp_aggregator.StructureGeneratorAgent","message":"Last aggregator closing, shutting down all persistent connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:44:07.615449","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"Disconnecting all persistent server connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:44:07.616260","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"command-executor: Requesting shutdown..."}
{"level":"INFO","timestamp":"2025-09-04T19:44:07.817481","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"All persistent server connections signaled to disconnect."}
{"level":"INFO","timestamp":"2025-09-04T19:44:07.817642","namespace":"mcp_agent.mcp.mcp_aggregator.StructureGeneratorAgent","message":"Connection manager successfully closed and removed from context"}
{"level":"INFO","timestamp":"2025-09-04T19:44:10.490545","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"code-implementation: Up and running with a persistent connection!"}
{"level":"INFO","timestamp":"2025-09-04T19:44:10.490990","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"code-reference-indexer: Up and running with a persistent connection!"}
{"level":"INFO","timestamp":"2025-09-04T19:44:10.912116","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"set_workspace","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:44:30.700205","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"execute_bash","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:44:38.590750","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"execute_bash","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:44:58.178345","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_multiple_files","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:45:48.234809","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_multiple_files","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:47:15.518480","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_multiple_files","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:47:26.674426","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"execute_python","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:47:35.888615","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:47:35.904134","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:48:07.377551","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:48:53.741360","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:49:18.582942","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:49:18.594808","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:51:18.266914","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_multiple_files","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:52:53.182209","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:53:34.812953","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:55:13.831277","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"write_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:55:36.569706","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:55:56.854185","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_code_mem","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:55:56.871152","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Requesting tool call","data":{"data":{"progress_action":"Calling Tool","tool_name":"read_file","server_name":"code-implementation","agent_name":"CodeImplementationAgent"}}}
{"level":"INFO","timestamp":"2025-09-04T19:58:15.794907","namespace":"mcp_agent.mcp.mcp_aggregator.CodeImplementationAgent","message":"Last aggregator closing, shutting down all persistent connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:58:15.795018","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"Disconnecting all persistent server connections..."}
{"level":"INFO","timestamp":"2025-09-04T19:58:15.795428","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"code-implementation: Requesting shutdown..."}
{"level":"INFO","timestamp":"2025-09-04T19:58:15.795499","namespace":"mcp_agent.mcp.mcp_connection_manager","message":"code-reference-indexer: Requesting shutdown..."}


### Additional Information

- DeepCode Version: Latest github source
- Operating System: MacOS
- Python Version:  3.13.2


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Uh oh!

[Bug]: Just stops on one error during code implementation stage. #39

Do you need to file an issue?

Describe the bug

Steps to reproduce

Expected Behavior

DeepCode Config Used

Default search server configuration

Options: "brave" or "bocha-mcp"

Planning mode configuration

Options: "segmented" or "traditional"

segmented: Breaks down large tasks to avoid token truncation (recommended)

traditional: Uses parallel agents but may hit token limits

Document segmentation configuration

If document size > threshold and enabled=true, use segmentation workflow

If document size <= threshold or enabled=false, use traditional full-document reading

Secrets (API keys, etc.) are stored in an mcp_agent.secrets.yaml file which can be gitignored

default_model: "o3-mini"

Logs and screenshots

Additional Information

Metadata

Assignees

Labels

Type

Projects

Milestone

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Development

[Bug]: Just stops on one error during code implementation stage. #39

Description

Do you need to file an issue?

Describe the bug

Steps to reproduce

Expected Behavior

DeepCode Config Used

Default search server configuration

Options: "brave" or "bocha-mcp"

Planning mode configuration

Options: "segmented" or "traditional"

segmented: Breaks down large tasks to avoid token truncation (recommended)

traditional: Uses parallel agents but may hit token limits

Document segmentation configuration

If document size > threshold and enabled=true, use segmentation workflow

If document size <= threshold or enabled=false, use traditional full-document reading

Secrets (API keys, etc.) are stored in an mcp_agent.secrets.yaml file which can be gitignored

default_model: "o3-mini"

Logs and screenshots

Additional Information

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions