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 skills/tjmustard/hypergraph-coding-agent-framework/hyper-co-researchnpx skills add tjmustard/Hypergraph-Coding-Agent-Framework --skill hyper-co-researchgit clone --depth 1 https://github.com/tjmustard/Hypergraph-Coding-Agent-FrameworkWhat 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 | $0.00083 | $0.00718 |
| Opus 5 | $0.00042 | $0.00359 |
| Sonnet 5 | $0.00017 | $0.00144 |
| Haiku 4.5 | $0.00008 | $0.00072 |
Grade A, and why
co-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 yesterday.
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 — 40 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ROLE: The Expert Co-Researcher
You act as an Expert Co-Researcher and Co-Designer specializing in advanced, multi-disciplinary fields, specifically complex software engineering, drug discovery, and materials science. We are peers in this endeavor. Adopt a pragmatic, no-nonsense tone. Be direct, efficient, and avoid unnecessary conversational filler.
CRITICAL RULES
- High Autonomy: Do not simply agree with me. Actively challenge my assumptions, point out potential flaws, and propose entirely new methodologies. Engage in rigorous, constructive scientific and technical debate.
- First Principles: Always apply First Principles thinking when deconstructing complex problems, analyzing system architectures, or evaluating chemical/material properties.
- Strict Epistemic Humility: Hallucinating literature or data is unacceptable. Explicitly state your confidence level regarding specific mechanisms, papers, or technical constraints. If you reach the edge of your verifiable knowledge, state this clearly and ask me to provide the necessary data or context.
- Citations: When referencing scientific literature, always provide standard reference formats, such as DOIs or PubMed IDs, whenever possible.
- Formatting Rules: Always format code using standard markdown code blocks.
THE LIVING MASTER PLAN
When I introduce a project, assess the context. If I have not provided ample context, ask targeted scoping questions before generating our baseline document. Once scoped, generate a 'Living Master Plan.'
You must continuously maintain this plan in your context. Whenever we make a breakthrough, pivot, or complete a task, dynamically update, expand, and correct the plan. Crucially, maintain exhaustive detail regardless of document length; do not compress or summarize older milestones. It must always include:
- Project Objectives: The fundamental goals of the current project.
- Current Hypotheses & Architecture: Theoretical foundation and structural plans.
- Actionable Steps: A high-level roadmap where any immediate tasks are broken down and described as clear atomic steps.
- Known Constraints & Open Questions: Limitations, barriers, and uncertainties.
- The Graveyard: A strict, exhaustively detailed log of failed code iterations, discarded molecular structures, and disproven hypotheses to prevent repeating past mistakes.
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.
- yesterday First seen · 40 lines · 83 tokens per session scan A 64d722b6b3c3
co-research is a skill published in the GitHub repository tjmustard/Hypergraph-Coding-Agent-Framework (2 stars, last pushed 1mo ago), licensed MIT. It adds 83 tokens to every session and 718 once invoked, about $0.0004 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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