[BUG] Local stdio MCP server connects but tools never registered as deferred tools (v2.1.97)

Summary

Local stdio MCP servers show ✓ Connected in claude mcp list but their tools are never registered as deferred tools — ToolSearch returns nothing for them. HTTP-transport MCP servers work correctly in the same session, proving this is specific to stdio transport, not MCP registration in general.

This is the same class of bug reported (and auto-closed as duplicates) in: #36914, #24762, #16371, #27159, #25894, #12474, #5241, #3426, #2682, #14807, #12164. Filing a fresh issue because the canonical #24762 was closed by the stale-bot and then auto-locked, per its own closing message instructing users to open a new issue.

Environment

• Claude Code version: 2.1.97
• Platform: macOS 26.2 (Darwin 25.2.0, arm64)
• Shell: fish
• Transport affected: stdio (local)
• Transport NOT affected: HTTP (remote)

Repro

Any local stdio MCP server will do. My repro uses a plugin-provided server:

$ claude mcp list
claude.ai Atlassian: https://mcp.atlassian.com/v1/sse - ✓ Connected
plugin:atlassian:atlassian: https://mcp.atlassian.com/v1/mcp (HTTP) - ✓ Connected
plugin:figma:figma: https://mcp.figma.com/mcp (HTTP) - ✓ Connected
plugin:elmq:elmq: /Users/casey/.claude/plugins/cache/elmq/elmq/0.1.0/target/release/elmq mcp - ✓ Connected

All four servers report connected. Inside the session:

• ToolSearch("atlassian") → returns mcp__plugin_atlassian_atlassian__* tools ✓
• ToolSearch("figma") → returns mcp__plugin_figma_figma__* tools ✓
• ToolSearch("elmq") → no results ✗
• ToolSearch("elm") → no results ✗
• ToolSearch("elm_summary") → no results ✗

The HTTP servers and the stdio server are all registered the same way (plugin mcpServers block in plugin.json). The only difference is transport.

Expected

stdio server's tools should be discoverable via ToolSearch and callable by the model, same as HTTP-transport MCP servers.

Actual

• claude mcp list shows ✓ Connected
• Server process is launched and stays alive
• Tools never appear in ToolSearch for the model
• Model cannot call any tool from the server

Why this matters

Every Claude Code plugin that ships a stdio MCP server is currently broken for affected users. Plugin authors have no workaround except telling users to install a global CLI and hope resolution happens to work out. The bug has been filed repeatedly since early 2024 (#2682 is 18+ months old), auto-closed as duplicates, and the canonical tracking issue is now locked. A lot of real-user reports have been silenced by the dedup bot without a fix ever landing.

Please assign this to a human rather than routing to dedup-bot.