[BUG] MCP tools (Notion, Slack, and other configured MCP servers) are unreliable in Claude Code cloud env sessions

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?

MCP tools (Notion, Slack, and other configured MCP servers) are unreliable in Claude Code Cloud Environment sessions:

1. Delayed registration — At session start, ToolSearch returns no results for MCP tools. They appear in a later system-reminder after the MCP server finishes connecting, but the assistant has already told the user that no MCP tools exist.
2. Repeated disconnections — All MCP servers disconnect and reconnect multiple times mid-conversation, making them unusable during gaps.
3. Complete absence in subagent sessions — Subagents spawned via the Agent tool never receive MCP tools. Only base deferred tools (AskUserQuestion, TodoWrite, etc.) are registered for them.

What Should Happen?

• MCP tools should be discoverable via ToolSearch from the first user message, or the assistant should be informed that MCP servers are still connecting.
• MCP servers should maintain stable connections throughout a session.
• Subagent sessions should inherit MCP tool access from the parent session.

Error Messages/Logs

No explicit error messages are surfaced to the user or assistant. The failures are silent:

1. DELAYED REGISTRATION (session start):
   - Assistant calls: ToolSearch(query="notion")
   - Response: "No matching deferred tools found"
   - No error, no "connecting..." indicator — just empty results
   - Tools appear silently in a later system-reminder

2. REPEATED DISCONNECTIONS (mid-session):
   - System-reminder arrives: "The following deferred tools are no longer available 
     (their MCP server disconnected). Do not search for them — ToolSearch will 
     return no match: mcp__fb5f90cd-...__notion-search, [60+ tools listed]"
   - Minutes later, another system-reminder: "The following deferred tools are now 
     available via ToolSearch."
   - This cycle repeated 3+ times in a single ~15 minute conversation.
   - All 3 MCP servers (Notion fb5f90cd-*, Slack da116102-*, and 66450a78-*) 
     always disconnect and reconnect together.

3. SUBAGENT ABSENCE:
   - Subagent runs ToolSearch(query="notion") — returns no results
   - Subagent's only deferred tools: AskUserQuestion, ExitPlanMode, Monitor, 
     NotebookEdit, RemoteTrigger, TodoWrite, WebFetch, WebSearch
   - No MCP tools are ever registered for the subagent session
   - Subagent tries WebFetch on Notion URL — gets HTTP 403 (expected, 
     since it's private/authenticated)

Steps to Reproduce

1. Configure Notion MCP (and optionally Slack + other MCP servers) in Claude Code web
2. Start a new session
3. Immediately ask: "Use the Notion MCP to search for X"
4. The assistant runs ToolSearch with query "notion" — returns no results
5. The assistant tells you no Notion MCP is configured
6. Moments later, a system-reminder appears listing all MCP tools as available
7. Additionally: during the session, all MCP servers disconnect and reconnect multiple times (observed 2+ disconnect/reconnect cycles in a single conversation)
8. Additionally: spawn a subagent via the Agent tool and ask it to use MCP tools — it will never find them

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

Not Sure

Claude Code Version

Claude 1.1617.0 (8d6345) 2026-04-09T16:10:15.000Z

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

• All three configured MCP servers (Notion fb5f90cd-, Slack da116102-, and 66450a78-*) connect and disconnect in unison, suggesting a shared transport/lifecycle issue rather than an individual server problem.
• The subagent issue is particularly impactful since it makes it impossible to delegate MCP-dependent work to background agents.

Claude-code itself has compiled this information for me, its hard to tell if what it claims is correct.