claude.ai managed MCP servers unavailable in --print mode since v2.1.79

Description

claude.ai managed MCP servers (Slack, Atlassian, Gmail, Google Calendar, Figma, etc.) stopped being available in headless --print mode starting from version 2.1.79. They work correctly in interactive mode and in --print mode on version 2.1.78.

Steps to reproduce

1. Configure claude.ai managed MCP servers (e.g., Slack, Atlassian) via https://claude.ai/settings/connectors
2. Verify they are connected: claude mcp list → shows ✓ Connected
3. Run in headless mode:

``bash
claude --print -p "List all tool names containing 'slack' or 'atlassian'" --output-format json --max-turns 1
``

1. No MCP tools are available in the output

Expected behavior

claude.ai managed MCP servers should be available in --print mode, as they were in v2.1.78.

Actual behavior

Only built-in tools (Bash, Read, Edit, Glob, Grep, etc.) and deferred tools are available. No mcp__claude_ai_* tools appear.

Environment

• Working version: 2.1.78 (installed 2026-03-18)
• Broken version: 2.1.79 (installed 2026-03-19), also broken in 2.1.80
• OS: macOS (Darwin 25.3.0)
• Auth: claude.ai account (Team subscription), claude auth status shows loggedIn: true
• Install method: native

Workaround

Pin to version 2.1.78:

ln -sf ~/.local/share/claude/versions/2.1.78 ~/.local/bin/claude

Impact

Breaks any automation relying on claude --print with cloud-hosted MCP integrations (Slack, Atlassian/Jira, etc.).