Raw scan report

Clio Kit — the complete, unedited output of the deterministic mcptrustchecker engine v1.13.0, scanned . Every finding, capability tag and score component below is exactly what the engine produced — no AI, no post-processing.

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{
  "tool": {
    "name": "mcptrustchecker",
    "version": "1.13.0",
    "methodologyVersion": "mcptrustchecker-1.13"
  },
  "target": {
    "id": "clio-kit",
    "source": {
      "kind": "package",
      "origin": "clio-kit"
    },
    "server": {
      "name": "clio-kit"
    }
  },
  "grade": "A",
  "score": {
    "score": 93,
    "threatScore": 100,
    "grade": "A",
    "band": "A",
    "categorySubtotals": {
      "injection": 0,
      "exfiltration": 0,
      "permissions": 0,
      "supply-chain": 0,
      "network": 0,
      "hygiene": 0
    },
    "vector": [
      {
        "kind": "client",
        "term": "capability-exposure",
        "level": "high",
        "label": "capability blast radius (high) — client exposure if the model is manipulated",
        "appliedPenalty": 6
      },
      {
        "kind": "client",
        "term": "verification-discount",
        "level": "repo",
        "label": "publisher verification (public source) — no provenance, but the source is public and inspectable",
        "appliedPenalty": 1
      },
      {
        "kind": "client",
        "term": "coverage-honesty",
        "level": "source",
        "label": "inspection depth (source) — how much of the target the scan could see",
        "appliedPenalty": 0
      }
    ],
    "gatesFired": [],
    "methodologyVersion": "mcptrustchecker-1.13"
  },
  "capability": {
    "level": "high",
    "reasons": [
      "ingests untrusted external content (a prompt-injection entry point)",
      "can send data / act on an external service",
      "can execute shell commands or code"
    ],
    "tags": [
      "external-sink",
      "untrusted-input",
      "code-exec"
    ]
  },
  "coverage": {
    "level": "source",
    "inputs": {
      "toolSurface": true,
      "implementationSource": true,
      "packageMetadata": true,
      "liveTransport": false
    },
    "caveats": [
      "Tools were statically extracted from the published source (154 recovered), not enumerated from a running server. Tool-poisoning, Unicode-smuggling, capability and toxic-flow analysis ran on this inferred surface, but a mis-parsed registration could be missed or mis-attributed, so tool-derived findings are capped below “confirmed”. To grade the real runtime surface, scan the running server: --command \"npx -y <package>\"."
    ]
  },
  "findings": [
    {
      "ruleId": "MTC-SRC-001",
      "title": "Dynamic code execution in server code (clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py:943`): Evaluating strings as code is the most direct RCE primitive; if any tool input reaches it, the server executes attacker-chosen code. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py"
      },
      "evidence": "slice_obj = eval(f\"np.s_[{slice_spec}]\") except Exception: return f\"Error: Invalid slice",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-001",
        "file": "clio-kit-mcp-servers/hdf5/src/hdf5_mcp/server.py",
        "line": 943,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-agentic-search/src/clio_agentic_search/tasks.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-agentic-search/src/clio_agentic_search/tasks.py:9`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-agentic-search/src/clio_agentic_search/tasks.py"
      },
      "evidence": "-> int: completed = subprocess.run(command, check=False) return completed.returncode def lint() -> None: r",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-agentic-search/src/clio_agentic_search/tasks.py",
        "line": 9,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py:34`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py"
      },
      "evidence": "r(cmd_args): proc = subprocess.run( cmd_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/chronolog/src/chronomcp/utils/helpers.py",
        "line": 34,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py:2322`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py"
      },
      "evidence": ": process = subprocess.Popen( argv, stdin=stdin_file, stdout",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/jarvis/src/jarvis_mcp/capabilities/jarvis_handler.py",
        "line": 2322,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py:99`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py"
      },
      "evidence": "SystemExit(125) child = subprocess.Popen(command, shell=message[\"shell\"], stdin=descriptor) raise SystemExit(child.wait(",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/jarvis/src/jarvis_mcp/windows_job.py",
        "line": 99,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py:168`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py"
      },
      "evidence": "ry: completed = subprocess.run( command, check=False, capture_output=True,",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/ndp/src/ndp_mcp/server.py",
        "line": 168,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py:216`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py"
      },
      "evidence": "ommand result = subprocess.run( ssh_cmd, capture_output=True, text=True,",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/remote_node_info.py",
        "line": 216,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in server code (clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py)",
      "category": "permissions",
      "severity": "high",
      "confidence": "strong",
      "description": "In the server's implementation (`clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py:35`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py"
      },
      "evidence": "try: result = subprocess.run( command, capture_output=True, text=True, timeout=timeout )",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/node-hardware/src/node_hardware_mcp/capabilities/utils.py",
        "line": 35,
        "nonRuntime": false
      }
    },
    {
      "ruleId": "MTC-FLOW-005",
      "title": "Untrusted input can drive an external action",
      "category": "exfiltration",
      "severity": "medium",
      "confidence": "strong",
      "description": "Untrusted-input tools ([download_paper_pdf, download_multiple_pdfs]) co-exist with external-action tools ([export_to_bibtex, export_to_json, export_to_csv, export_to_text]). A prompt injection could cause unwanted external actions, though no direct sensitive-data leak path was found.",
      "remediation": "Require confirmation for state-changing/egress actions triggered after processing untrusted content.",
      "location": {
        "kind": "flow",
        "name": "download_paper_pdf → export_to_bibtex"
      },
      "evidence": "untrusted [download_paper_pdf, download_multiple_pdfs] → sinks [export_to_bibtex, export_to_json, export_to_csv, export_to_text]",
      "owasp": "LLM06:2025 Excessive Agency",
      "references": [],
      "data": {
        "untrusted": [
          "download_paper_pdf",
          "download_multiple_pdfs"
        ],
        "sinks": [
          "export_to_bibtex",
          "export_to_json",
          "export_to_csv",
          "export_to_text"
        ]
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py)",
      "category": "permissions",
      "severity": "low",
      "confidence": "heuristic",
      "description": "In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py:36`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py"
      },
      "evidence": "self.process = subprocess.Popen( command, stdin=subprocess.PIPE, stdout=sub",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/jarvis/scripts/live_ares_semantic_mcp_probe.py",
        "line": 36,
        "nonRuntime": true
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/paraview/scripts/automate_setup.py)",
      "category": "permissions",
      "severity": "low",
      "confidence": "heuristic",
      "description": "In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/paraview/scripts/automate_setup.py:52`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/paraview/scripts/automate_setup.py"
      },
      "evidence": "process = subprocess.Popen( cmd, cwd=cwd or self.project_root,",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/paraview/scripts/automate_setup.py",
        "line": 52,
        "nonRuntime": true
      }
    },
    {
      "ruleId": "MTC-SRC-002",
      "title": "Shell/command execution in packaging/dev tooling (clio-kit-mcp-servers/paraview/scripts/build_paraview.py)",
      "category": "permissions",
      "severity": "low",
      "confidence": "heuristic",
      "description": "In a packaging/dev/install script (shipped, but not the server runtime) (`clio-kit-mcp-servers/paraview/scripts/build_paraview.py:23`): Spawning a shell/process is command-execution capability; with unsanitized tool input it is command injection / RCE. This is read from the code itself — not from the tool description — so a poisoned server cannot hide it behind honest-looking metadata.",
      "remediation": "Review this call path: confirm it never receives unsanitized tool input, constrain it, or remove it. Treat a server whose code reaches these sinks as high-capability regardless of what its tools claim.",
      "location": {
        "kind": "server",
        "name": "clio-kit-mcp-servers/paraview/scripts/build_paraview.py"
      },
      "evidence": "d.split() result = subprocess.run(cmd, cwd=cwd, capture_output=False, text=True) if check and result.returncode",
      "owasp": "LLM05:2025 Improper Output Handling",
      "data": {
        "rule": "MTC-SRC-002",
        "file": "clio-kit-mcp-servers/paraview/scripts/build_paraview.py",
        "line": 23,
        "nonRuntime": true
      }
    }
  ],
  "toxicFlows": [
    {
      "id": "flow-1",
      "severity": "medium",
      "confidence": "strong",
      "untrustedInput": [
        "download_paper_pdf",
        "download_multiple_pdfs"
      ],
      "sensitiveSource": [],
      "externalSink": [
        "export_to_bibtex",
        "export_to_json",
        "export_to_csv",
        "export_to_text"
      ],
      "selfContained": false,
      "description": "Untrusted input can drive an external action even though no sensitive source is exposed."
    }
  ],
  "capabilities": [
    {
      "tool": "list_bp5",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "inspect_variables",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "inspect_variables_at_step",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "inspect_attributes",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "read_variable_at_step",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_arxiv",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_recent_papers",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_papers_by_author",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_by_title",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_by_abstract",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_by_subject",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "search_date_range",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_paper_details",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "export_to_bibtex",
      "tags": [
        "external-sink"
      ],
      "reasons": {
        "external-sink": [
          "keyword \"export_to\""
        ]
      }
    },
    {
      "tool": "find_similar_papers",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "download_paper_pdf",
      "tags": [
        "untrusted-input"
      ],
      "reasons": {
        "untrusted-input": [
          "keyword \"download\""
        ]
      }
    },
    {
      "tool": "get_pdf_url",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "download_multiple_pdfs",
      "tags": [
        "untrusted-input"
      ],
      "reasons": {
        "untrusted-input": [
          "keyword \"download\""
        ]
      }
    },
    {
      "tool": "start_chronolog",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "record_interaction",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "stop_chronolog",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "retrieve_interaction",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "compress_file_tool",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "decompress_file_tool",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "load_darshan_log",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_job_summary",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "analyze_file_access_patterns",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_io_performance_metrics",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "analyze_posix_operations",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "analyze_mpiio_operations",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "identify_io_bottlenecks",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_timeline_analysis",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "compare_darshan_logs",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "generate_io_summary_report",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "refresh_hdf5_resources",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "list_available_hdf5_files",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "update_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "build_pipeline_env",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "create_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "load_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "export_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "get_pkg_config",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "append_pkg",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "configure_pkg",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "run_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "destroy_pipeline",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "jm_create_config",
      "tags": [],
      "reasons": {}
    },
    {
      "tool": "jm_load_config",
      "tags": [],
      "reasons": {}
    },
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