Custom MCP server tools not available despite successful connection

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Custom MCP servers connect successfully (shown in /mcp and claude mcp list),
but their tools are not available to Claude. Only built-in MCP servers
(perplexity, claude-in-chrome, ide) have functional tools.

What Should Happen?

Tools from connected custom MCP servers should be available, as they were
before recent updates.

Error Messages/Logs

Steps to Reproduce

1. Configure a custom MCP server (tested with both SSE and HTTP transports):

claude mcp add --transport sse maverick-mcp http://localhost:8003/sse

1. Verify connection: claude mcp list shows ✓ Connected
2. Start a conversation and attempt to use any tool from the custom server
3. Tools fail with: Error: No such tool available:

mcp__maverick-mcp__<tool_name>

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

version: 2.1.19

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

Actual Behavior

• Server shows ✓ Connected in /mcp view
• ListMcpResourcesTool can query the server successfully
• Server responds to MCP protocol messages (initialize, tools/list)
• But no tools from the custom server are available to Claude
• ToolSearch returns "No matching deferred tools found" for custom server

tools

Troubleshooting Attempted
Approach: SSE transport
Result: Connected, tools unavailable
────────────────────────────────────────
Approach: HTTP (Streamable) transport
Result: Connected, tools unavailable
────────────────────────────────────────
Approach: ENABLE_TOOL_SEARCH=false
Result: No change
────────────────────────────────────────
Approach: Server restart
Result: No change
────────────────────────────────────────
Approach: Claude Code restart
Result: No change
────────────────────────────────────────
Approach: Verified server exposes tools via MCP protocol
Result: Tools exist on server
Server Verification

Direct MCP protocol query confirms tools are registered:
curl -X POST "http://localhost:8003/mcp/" \
-H "Content-Type: application/json" \
-H "Accept: application/json, text/event-stream" \
-d '{"jsonrpc":"2.0","method":"initialize","id":1,...}'
# Returns: serverInfo: {name: "MaverickMCP", version: "1.15.0"},
capabilities: {tools: {listChanged: true}}

Regression

This worked previously. The issue appeared after recent Claude Code updates
(possibly related to ToolSearch/deferred tools changes).

Related

• Issue #20307 (SSE deprecation documentation) — mentions SSE deprecation

but this affects HTTP transport equally

Additional Context

• Built-in MCP servers (perplexity, claude-in-chrome) work correctly
• Custom server is FastMCP-based with 35+ tools registered
• Server logs confirm tools are registered at startup