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.
{
"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": {}
},
{
"tool": "jm_save_config",
"tags": [],
"reasons": {}
},
{
"tool": "jm_set_hostfile",
"tags": [],
"reasons": {}
},
{
"tool": "jm_bootstrap_from",
"tags": [],
"reasons": {}
},
{
"tool": "jm_bootstrap_list",
"tags": [],
"reasons": {}
},
{
"tool": "jm_list_pipelines",
"tags": [],
"reasons": {}
},
{
"tool": "jm_cd",
"tags": [],
"reasons": {}
},
{
"tool": "jm_list_repos",
"tags": [],
"reasons": {}
},
{
"tool": "jm_add_repo",
"tags": [],
"reasons": {}
},
{
"tool": "jm_remove_repo",
"tags": [],
"reasons": {}
},
{
"tool": "jm_promote_repo",
"tags": [],
"reasons": {}
},
{
"tool": "jm_get_repo",
"tags": [],
"reasons": {}
},
{
"tool": "jm_construct_pkg",
"tags": [],
"reasons": {}
},
{
"tool": "jm_graph_show",
"tags": [],
"reasons": {}
},
{
"tool": "jm_graph_build",
"tags": [],
"reasons": {}
},
{
"tool": "jm_graph_modify",
"tags": [],
"reasons": {}
},
{
"tool": "module_list",
"tags": [],
"reasons": {}
},
{
"tool": "module_avail",
"tags": [],
"reasons": {}
},
{
"tool": "module_show",
"tags": [],
"reasons": {}
},
{
"tool": "module_load",
"tags": [],
"reasons": {}
},
{
"tool": "module_unload",
"tags": [],
"reasons": {}
},
{
"tool": "module_swap",
"tags": [],
"reasons": {}
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