MCP vs CLI for AI Agents: A Comparative Analysis of Tool Integration Strategies for Autonomous Systems

arXiv cs.AIOctober 23, 2026en

arXiv:2610.30157v1 Announce Type: new Abstract: AI agents require interfaces to interact with external systems such as files, APIs, databases, and cloud services. Two competing paradigms have emerged: CLI (Command Line Interface), where agents execute shell commands directly, and MCP (Model Context Protocol), a structured JSON-RPC protocol providing governed, typed tool access. This paper presents a comparative analysis across 14 evaluation dimensions, supported by worked examples, security assessment against established compliance frameworks, and economic modeling. Our analysis indicates that CLI provides superior efficiency for single-user, local-only workflows, while MCP addresses require

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