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clio-kit

clio-kit is a plugin for Gemini CLI from iowarp/clio-kit. Its token cost is not measured, scanned A, original, BSD-3-Clause.

A collection of 24 MCP servers for tasks including research archives, scientific data formats, compression, geospatial data, and system tools. MCP is a standard way for an AI assistant to connect to external tools.

In plain words
What is it for?
It helps an agent access services such as arXiv, HDF5, GeoJSON, geospatial tools, and other listed servers.
Why use it?
It gathers many specialized tool connections under one configuration instead of requiring each server to be set up separately.

Plugin for Gemini CLI

Written for Gemini CLI: a Gemini CLI extension manifest.

not rated 30repo changed 4d ago A scan tokens not measured original BSD-3-Clause

Good fit It helps an agent access services such as arXiv, HDF5, GeoJSON, geospatial tools, and other listed servers.

Compare 6 plugins from other repositories ↓
Install with agentmods
npx agentmods add plugins/iowarp/clio-kit/gemini-extension
View source ↗ iowarp/clio-kit toolkit.iowarp.ai
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo
git clone --depth 1 https://github.com/iowarp/clio-kit

Made for: Gemini CLI.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for clio-kit

README.md
[![agentmods](https://agentmods.dev/badge/plugins/iowarp/clio-kit/gemini-extension/github.svg)](https://agentmods.dev/plugins/iowarp/clio-kit/gemini-extension)
Your own site
<a href="https://agentmods.dev/plugins/iowarp/clio-kit/gemini-extension"><img src="https://agentmods.dev/badge/plugins/iowarp/clio-kit/gemini-extension/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for clio-kit

Your own site · 80×15
<a href="https://agentmods.dev/plugins/iowarp/clio-kit/gemini-extension"><img src="https://agentmods.dev/badge/plugins/iowarp/clio-kit/gemini-extension.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session not measured What this adds to a session before it is invoked.
When invoked not measured Not applicable: nothing here is loaded into a session.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Security

Grade A, and why

clio-kit scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.

The scan reads gemini-extension.json. This mod also ships 12 executable files (scripts/assert_no_skipped_tests.py, scripts/check_baseline_diff.py, scripts/check_file_size.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

gemini-extension.json · 175 lines

How it starts

The opening of the file, as written. The whole thing — 175 lines — stays where its author put it; the contents beside it link to each section on GitHub.

{
  "name": "clio-kit",
  "version": "2.7.2",
  "mcpServers": {
    "clio-adios": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "adios"
      ]
    },
    "clio-arxiv": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "arxiv"
      ]
    },
    "clio-chronolog": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "chronolog"
      ]
    },
    "clio-compression": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "compression"
      ]
    },
    "clio-darshan": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "darshan"
      ]
    },
    "clio-geo": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "geo"
      ]
    },
    "clio-geojson": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "geojson"
      ]
    },
    "clio-hdf5": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "hdf5"
      ]
    },
    "clio-jarvis": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "jarvis"
      ]
    },
    "clio-lmod": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "lmod"
      ]
    },
    "clio-ndp": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "ndp"
      ]
    },
    "clio-node-hardware": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "node-hardware"
      ]
    },
    "clio-pandas": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "pandas"
      ]
    },
    "clio-parallel-sort": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "parallel-sort"
      ]
    },
    "clio-paraview": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "paraview"
      ]
    },
    "clio-parquet": {
      "command": "clio-kit",
      "args": [
        "mcp-server",
        "parquet"

Read the full file on GitHub · 175 lines

Files

What ships with it

12 files beside gemini-extension.json in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 4d ago Changed 7c15097ac747
  2. 1mo ago First seen · 175 lines scan A 4ec38f1e0255

Subscribe to this mod's changes

clio-kit is a plugin published in the GitHub repository iowarp/clio-kit (30 stars, last pushed 2d ago), licensed BSD-3-Clause. Its token cost is not measured: this kind of file is read by the harness, not the model. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-06.

ResearchScientificai4hpcai4sciencehpchpc-aimcpmcp-tools
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