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Add comprehensive excluded methods section to MCP ARCHITECTURE.md categorizing all 105 excluded RPC methods by reason (wrong context, CLI tooling, registry admin, tunnel mgmt, security, etc.). Remove system.shell tool — host-level shell access is too broad a privilege for MCP agents. Agents can still exec into package subcontainers via package.shell. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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