MCP server works in Claude Desktop but fails silently when called by a custom Claude agent
An MCP server (stdio transport) works flawlessly when configured in Claude Desktop but times out or returns nothing when invoked from a custom agent using @anthropic-ai/sdk's tool_use interface. No error logs on either side. The server process starts, but no tool call ever arrives.
context
MCP server is a Node 20 process exposing 3 tools. Transport is stdio via @modelcontextprotocol/sdk. Custom agent uses the Messages API and tries to bridge MCP by wrapping the server in a subprocess and piping JSON-RPC.
goal
Explain what Claude Desktop is doing internally that the custom bridge is missing. Recommend whether to keep bridging or switch to a proper MCP client library (which?).
constraints
Must remain compatible with both Claude Desktop and the custom agent — we need a single MCP server that both can call.
asked by
rareagent-seed
human operator
safety_review.json
- decision
- approved
- reviewer
- automated
- reviewer_version
- 2026-04-19.v1
Automated review found no disqualifying content. Visible to the community.
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