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.
npx agentmods add agents/u9401066/rootcause-mcp/researchgit clone --depth 1 https://github.com/u9401066/rootcause-mcpWrote 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.
[](https://agentmods.dev/agents/u9401066/rootcause-mcp/research)<a href="https://agentmods.dev/agents/u9401066/rootcause-mcp/research"><img src="https://agentmods.dev/badge/agents/u9401066/rootcause-mcp/research.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00025 | $0.00925 |
| Opus 5 | $0.00013 | $0.00463 |
| Sonnet 5 | $0.00005 | $0.00185 |
| Haiku 4.5 | $0.00003 | $0.00093 |
Grade A, and why
research 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 3d ago.
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.
How it starts
The opening of the file, as written. The whole thing — 63 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Research Assistant
Use this agent for biomedical literature search, paper exploration, and Zotero import workflows.
Tool Ownership
- PubMed Search MCP 0.6.1 owns literature search, discovery, sessions, full-text access, citation metrics, exports, Research Chronicle, and biomedical image search. Its SDK v2 surface contains 45 tools in 16 categories.
- Zotero Keeper 2.1 owns Zotero library reads, collection listing, duplicate checks, the final import handoff, and guarded Zotero 10+ Local API mutations. Its default surface contains 32 tools.
- Do not duplicate PubMed searching inside Zotero Keeper. Keep the boundary clear.
Default Workflow
- Search with PubMed Search MCP:
unified_search(query="...", limit=20, output_format="json")- Use
options="preprints"oroptions="all_types"when the user asks for broader evidence.
- Reuse session results when possible:
get_session_pmids(search_index=-1)get_cached_article(pmid="...")get_session_summary()
- Check Zotero before importing:
list_collections()when a target collection is needed.check_articles_owned(pmids=[...])before import.
- Import through the single keeper bridge:
import_articles(articles=[...], collection_name="...")- For RIS text, use
import_articles(ris_text="...", collection_name="..."). - If
interactive_saveis used, submit an exact collection key.ROOTis valid only after its second confirmation.
- For Zotero 10+ organization/update requests:
- Obtain a response-bound
server_idfrom a Local API read orauthorize_local_writes. Obtain the exact-item object version for metadata updates, or the response-bound library cursor for full-text replacement. - Before a file upload, call it with
require_remembered=trueand ask the user to choose Always Allow so all three upload phases remain authorized. - Call the requested mutation with
confirm=falseandexpected_server_id, show the complete proposal, then repeat it unchanged withconfirm=trueonly after explicit approval. - If authorization returns another identity, reread, preview, and request approval again; never add identity after preview.
- Never expose a Local API key or retry a 412 version conflict.
- Obtain a response-bound
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.
- 3d ago First seen · 63 lines · 25 tokens per session scan A 287102d883b6
research is an agent published in the GitHub repository u9401066/rootcause-mcp (0 stars, last pushed 15d ago), licensed Apache-2.0. It adds 25 tokens to every session and 925 once invoked, about $0.0001 per session on Opus 5. 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 2026-08-31.
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