[BUG] claude.ai MCP connectors not available in -p / --print mode

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 servers connected via claude.ai native connectors (HTTP-based, OAuth-authenticated) show as "Connected" in claude mcp list but are completely unavailable when Claude Code runs in any non-interactive mode. The init message in stream-json output shows "mcp_servers":[], and the model has zero access to MCP tools.

This affects all programmatic invocation paths: --print, --output-format stream-json, and piped stdin.

What Should Happen?

MCP servers that are connected and healthy (verified via claude mcp list) should also be available when using -p / --print mode or --input-format stream-json. The mcp_servers array in the stream-json init message should list the same servers that appear in interactive mode.

Error Messages/Logs

Steps to Reproduce

1. Confirm MCP servers are connected:

claude mcp list
Output:
rube
Type: project
Status: connected
Protocol: HTTP (Streamable)
URL: https://rube.app/mcp
Tools: 11

claude_ai_Rube
Type: claude_ai
Status: connected
Protocol: HTTP (Streamable)
Tools: 11

claude_ai_Granola
Type: claude_ai
Status: connected
Protocol: HTTP (Streamable)
Tools: 4

claude_ai_Slack
Type: claude_ai
Status: connected
Protocol: HTTP (Streamable)
Tools: 12

1. Run in print mode -- no MCP tools available:

claude -p "List every tool you have access to that starts with mcp" --dangerously-skip-permissions
Result: Model lists only 17 core tools (Read, Write, Edit, Bash, Glob, Grep, etc.). Zero MCP tools.

1. Verify via stream-json init message:

claude -p "hello" --output-format stream-json --verbose --dangerously-skip-permissions
Init message contains:
{"type":"system","subtype":"init","mcp_servers":[], ...}

1. Also tested and confirmed broken:

claude --input-format stream-json with JSON piped via stdin
echo "test" | claude (piped stdin, non-TTY)
claude -p --mcp-config '{"mcpServers":{"rube":{"type":"http","url":"https://rube.app/mcp"}}}' -- tools appear in --mcp-config listing but mcp_servers:[] persists in init

1. Confirm it works interactively: Launch claude in a TTY terminal (VSCode integrated terminal). Same machine, same config. MCP servers connect and all tools are available.

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.14

Platform

Other

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

Claude subscription (not API key)
MCP server type: claude_ai (HTTP, OAuth-authenticated via claude.ai)

Impact
This blocks programmatic use of Claude Code for any workflow that depends on MCP tools. Our use case: wrapping existing CLI slash commands with a Slack bot so a team can invoke them without terminal access. The commands require Rube MCP (Dropbox, Gmail, Calendar, Sheets) to function.