[BUG] Cloud-hosted MCP tools (mcp__claude_ai_*) silently absent in pipe mode (-p) despite ENABLE_CLAUDEAI_MCP_SERVERS being enabled by default

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?

Cloud-hosted MCP tools (mcp__claude_ai_* — Slack, Notion, Vercel, Indeed, Gmail, Calendar, Snowflake, etc.) are completely absent from the system prompt when Claude Code runs in pipe mode (-p). These tools work perfectly in interactive CLI mode but are silently dropped in pipe/SDK mode.

The official docs state ENABLE_CLAUDEAI_MCP_SERVERS is "enabled by default for logged-in users" — but this default is not honored in pipe mode. Setting ENABLE_CLAUDEAI_MCP_SERVERS=true explicitly also has no effect.

Evidence from JSONL session files on the same machine, same user, same version (2.1.81), same model:

| | Interactive CLI | Pipe mode (-p) |
|---|---|---|
| entrypoint | "cli" | "sdk-cli" |
| system prompt tokens | ~128K | ~115K |
| cloud MCP tools | ✅ all present | ❌ none |
| local MCP tools | ✅ all present | ✅ all present |

The ~13K token difference corresponds exactly to the missing cloud MCP tool definitions.

What Should Happen?

Cloud-hosted MCP tools should be available in pipe mode for logged-in users, consistent with the documented behavior: "ENABLE_CLAUDEAI_MCP_SERVERS is enabled by default for logged-in users."

A flag like --enable-cloud-mcp or honoring ENABLE_CLAUDEAI_MCP_SERVERS=true in pipe mode would resolve this.

Error Messages/Logs

No error messages — the tools are silently absent with no warning.

Reproduction test:
$ claude -p "List tools starting with mcp__claude_ai_Slack. If none, say NONE FOUND."
→ NONE FOUND

$ ENABLE_CLAUDEAI_MCP_SERVERS=true claude -p "List tools starting with mcp__claude_ai_Slack. If none, say NONE FOUND."
→ NONE FOUND

Both return NONE FOUND despite being logged in and all cloud MCP tools working interactively.

Steps to Reproduce

1. Log into Claude Code with a claude.ai account (Claude Pro)
2. Verify cloud MCP tools work interactively:

$ claude
> List tools starting with "mcp__claude_ai_Slack"
→ Lists all Slack tools ✅

1. Test pipe mode:

$ claude -p "List tools starting with mcp__claude_ai_Slack. If none, say NONE FOUND."
→ NONE FOUND ❌

1. Test with explicit env var:

$ ENABLE_CLAUDEAI_MCP_SERVERS=true claude -p "List tools starting with mcp__claude_ai_Slack. If none, say NONE FOUND."
→ NONE FOUND ❌

1. Test fake TTY:

$ script -q /dev/null claude -p "List tools starting with mcp__claude_ai_Slack. If none, say NONE FOUND."
→ NONE FOUND ❌

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.81

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

This blocks any application built on top of Claude Code using -p or the @anthropic-ai/claude-code SDK from accessing cloud-hosted MCP integrations that the user has connected through their claude.ai account.

Use case: Building a web UI (Claude Lens) that spawns sessions via -p --output-format stream-json --input-format stream-json. Users expect the same MCP tools available in the terminal to work in the web UI — same machine, same auth, same binary.

Workarounds tested (all failed):

• ENABLE_CLAUDEAI_MCP_SERVERS=true — no effect
• Fake TTY via script -q /dev/null — no effect (not a TTY check)
• --input-format stream-json vs plain -p — no difference

Note: local MCP servers (mcp__github__, mcp__google-workspace__, mcp__notion-hq__) work correctly in pipe mode — only cloud-hosted mcp__claude_ai_ tools are affected.