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These tool calls are the agent's syscalls: privileged operations with side effects on shared state, yet today's safety enforcement lives entirely in userspace, where a 10-line script can bypass it. I propose Governed MCP, a kernel-resident tool governance gateway built on a logit-based safety primitive (ProbeLogits). The gateway interposes on every MCP tool call in a 6-layer pipeline: schema validation, trust tier, rate limit, adversarial pre-filter, a ProbeLogits semantic gate (the load-bearing check), and constitutional policy match, with a Blake3-hashed audit chain.\n  I implement Governed MCP in Anima OS, a bare-metal x86-64 kernel in ~286,000 lines of Rust. The five non-inference layers plus the audit append cost a measured 11.3 us per call; the ProbeLogits gate (one probe-prompt prefill plus a single logit read","title":"Governed MCP: Kernel-Level Tool Governance for AI Agents via Logit-Based Safety Primitives","url":"https://arxiv.org/abs/2604.16870","vendor":"arxiv_cs_ai"},"summary":"arXiv:2604.16870v2 Announce Type: replace-cross \nAbstract: AI agents increasingly call external tools (file system, network, APIs) through the Model Context Protocol (MCP). These tool calls are the agent's syscalls: privileged operations with side effects on shared state, yet today's safety enforcement lives entirely in userspace, where a 10-line script can bypass it. I propose Governed MCP, a kernel-resident tool governance gateway built on a logit-based safety primitive (ProbeLogits). The gateway interposes on every MCP tool call in a 6-layer pipeline: schema validation, trust tier, rate limit, adversarial pre-filter, a ProbeLogits semantic gate (the load-bearing check), and constitutional policy match, with a Blake3-hashed audit chain.\n  I implement Governed MCP in Anima OS, a bare-metal x86-64 kernel in ~286,000 lines of Rust. 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