Claude Code reads mcpServers from ~/.claude.json (global state file), NOT from ~/.claude/settings.json. The settings.json mcpServers key is silently ignored for MCP loading. Using claude mcp add --scope user writes to the correct file. Also document correct registration commands and scope semantics in RUNTIME.md so agents and users know how to add MCPs that actually load. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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