MCP tool responses return empty results for some tools while others work

Summary

The VectorCode MCP server's query tool returns empty results ({"result":[]}) when called through Claude Code, while other tools from the same server (like ls) work correctly. The server itself returns valid data when tested directly via stdio.

Reproduction Steps

1. Configure an MCP server in ~/.mcp.json:

{
  "mcpServers": {
    "vectorcode": {
      "command": "vectorcode-mcp-server",
      "args": []
    }
  }
}

1. Start Claude Code and call the ls tool:

mcp__vectorcode__ls()

Result: Returns valid data:

{"result":["/home/michel/Sites/unicstay/vacation"]}

1. Call the query tool:

mcp__vectorcode__query(query_messages=["booking"], n_query=2, project_root="/home/michel/Sites/unicstay/vacation")

Result: Returns empty:

{"result":[]}

1. Test the same query directly via stdio to the server:

echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"capabilities":{}}}
{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"query","arguments":{"query_messages":["booking"],"n_query":2,"project_root":"/home/michel/Sites/unicstay/vacation"}}}' | vectorcode-mcp-server

Result: Returns valid results:

{"jsonrpc":"2.0","id":2,"result":{"content":[{"type":"text","text":"{'path': './tests/Unit/BookingPreviewTest.php', ...}"}]}}

Expected Behavior

The query tool should return the same results through Claude Code that it returns when called directly via stdio.

Actual Behavior

• ls tool: Works correctly
• query tool: Returns empty {"result":[]}

Both tools use the same MCP server and connection. The server returns valid JSON-RPC responses for both, but Claude Code only parses the ls response correctly.

Environment

• Claude Code version: 2.1.31
• OS: Fedora Linux 43 (Linux 6.18.7)
• MCP server: VectorCode MCP server (FastMCP-based, Python)

Additional Context

The VectorCode MCP server is built with FastMCP (official MCP Python SDK). Both tools are exposed via the same @mcp.tool() decorator pattern. The ls tool returns a simple list of paths, while query returns a list of dictionaries with file paths and content.

This suggests the issue may be related to how Claude Code's MCP client parses certain response formats - specifically responses containing nested structures or larger text content.

Workaround

Using the CLI directly works:

cd /project/path && vectorcode query "keywords" -n 5