yes. each agent worktree gets its own .mcp.json built from the merged config in bernstein.yaml mcp: section plus the agent's own discovery (claude code reads ~/.config/claude/mcp.json, codex reads its own). bernstein passes mcp tool calls through transparently; it does not proxy them. the merger lives in src/bernstein/adapters/claude_mcp_loader.py. you can also expose bernstein itself as an mcp server (see mcp-server-for-multi-agent-coding) so a claude desktop session can dispatch coding tasks into a bernstein fleet via tool calls. mcp config is per task, so a security task can be given a different toolset than a docs task.
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