MCP Tools Always Return "No Relevant Documentation Found" for All Queries

[MohitY70]

I am trying to use the MCP tools for this repository:
https://github.com/MohitY70/secure-file-transfer-p2pp

However, none of the available tools are returning any meaningful response. Every tool I tested (against public repositories) consistently returns the same result:

### Search Results for: "src/Providers/SecureTransferServiceProvider.php"

No relevant documentation found for your query. It's either being indexed or the search query did not match any documentation.

As a fallback, this is the documentation for MohitY70/secure-file-transfer-p2p:

No documentation found.

If you'd like to retry the search, try changing the query to increase the likelihood of a match.

This happens for all MCP tools, regardless of:

• Repository (tested with multiple public repos)
• Query string
• Tool type (search, fetch, etc.)

It appears that the MCP server connects successfully, but the tools never return actual data.

---

🔁 Steps to Reproduce

1. Configure MCP server with a public GitHub repository.
2. Connect MCP Console to the server.
3. Use any available tool (e.g., search_secure_docs).
4. Provide a valid query such as:

{
  "query": "src/Providers/SecureTransferServiceProvider.php"
}

5. Execute the tool.

---

❌ Actual Behavior

Every tool execution returns:

• “No relevant documentation found”
• “No documentation found”
• Empty or fallback response

This occurs even when querying files that definitely exist in the repository.

---

✅ Expected Behavior

The tools should:

• Index the repository
• Return matching documentation or code snippets
• Provide meaningful search results instead of empty responses

---

🧪 Environment

• MCP Console: https://llm-mcp-webui.vercel.app/settings/mcp
• Repository used for testing: Public GitHub repositories
• Transport: http-direct
• Example repo tested:
  MohitY70/secure-file-transfer-p2p

---

Additional Notes

• The server status shows connected
• Tools are listed correctly in MCP Console
• Issue persists across multiple queries and repositories

Please let me know if any additional configuration is required.

[Basavaraj8143]

I tried analyzing this behavior — since the MCP server connects and tools execute but always return empty results, it seems like the issue might be in the indexing stage rather than search itself.

Is there a step where repository content is fetched and indexed before search is executed? If that step fails or doesn’t persist data, it could explain why all queries return fallback responses.

I’ll try to trace the indexing pipeline locally and update with findings.

[kth8]

All agent harnesses include a bash tool so I think the most reliable way to get docs/source code is just get your agent to clone the repo then it can explore it locally (using multiple sub-agents in parallel) instead of relying on an online service, plus minimize number of tools.