MCP codebase-retrieval tool discovered but "not found" on invocation

[nitedani]

Description

When using auggie --mcp as an MCP server with VS Code + GitHub Copilot in WSL, the codebase-retrieval tool is successfully discovered but fails with "Tool codebase-retrieval not found" when invoked.

Environment

• Auggie CLI: 0.11.0-prerelease.3 (commit 920184d0), installed at /usr/bin/auggie
• VS Code (Windows): 1.106.3, Commit: bf9252a2fb45be6893dd8870c0bf37e2e1766d61
• VS Code Server (WSL): 1.106.3
• GitHub Copilot: 1.388.0
• GitHub Copilot Chat: 0.33.4
• OS: Windows_NT x64 10.0.26200 + WSL: Ubuntu

MCP Configuration

Location: ~/.vscode-server/data/User/mcp.json

{
  "servers": {
    "augmentcode": {
      "type": "stdio",
      "command": "auggie",
      "args": ["--mcp", "-m", "default"]
    }
  }
}

Steps to Reproduce

1. Open VS Code connected to WSL (Ubuntu)
2. Configure the augmentcode MCP server as shown above
3. Start the MCP server
4. Verify server starts correctly (see logs below showing "Discovered 1 tools")
5. In Copilot Chat (Agent mode), attempt to use the codebase-retrieval tool
6. Observe the error: "Tool codebase-retrieval not found"

MCP Server Output Logs

Server starts successfully and tool is discovered:

2025-12-05 14:20:34.157 [warning] [server stderr] Stdio mode
2025-12-05 14:20:34.172 [warning] [server stderr] Starting workspace indexing in background...
2025-12-05 14:20:34.173 [warning] [server stderr] Available tools: codebase-retrieval
2025-12-05 14:20:34.173 [warning] [server stderr] Workspace indexing complete
2025-12-05 14:20:34.173 [warning] [server stderr] MCP tool server started
2025-12-05 14:20:34.174 [warning] [server stderr] Ready for MCP client connections
2025-12-05 14:20:34.181 [info] Discovered 1 tools

Tool Invocation Result

Input:
{
  "information_request": "What is the main architecture of this project?"
}
Output:

Tool codebase-retrieval not found.

Expected Behavior

When a tool is discovered by VS Code (as shown in logs), invoking that tool should work.

Actual Behavior

Tool invocation fails with "Tool codebase-retrieval not found" despite successful discovery.

Proof: Other WSL-native MCP Servers Work

Tested other MCP servers using WSL-native binaries (not npx) in the identical environment:

MCP Server	Command	Result
mcp-server-memory	uvx mcp-server-memory	✅ Works
mcp-server-sqlite	uvx mcp-server-sqlite	✅ Works
auggie --mcp	auggie --mcp -m default	❌ "Tool not found"

Conclusion: VS Code/Copilot MCP infrastructure works correctly with WSL binaries. The issue is specific to Auggie's MCP implementation.

Additional Notes

• The tool appears correctly in VS Code's "Configure Tools" dialog and is checked/enabled
• The MCP server shows "Running" status
• auggie works correctly when run directly in the terminal
• The Augment VS Code extension's native chat panel works fine (direct access to codebase-retrieval)