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 skills add a-attia/scicomp-research-skills --skill project-onboardinggit clone --depth 1 https://github.com/a-attia/scicomp-research-skillsWrote 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/skills/a-attia/scicomp-research-skills/project-onboarding)<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/project-onboarding"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/project-onboarding/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.
<a href="https://agentmods.dev/skills/a-attia/scicomp-research-skills/project-onboarding"><img src="https://agentmods.dev/badge/skills/a-attia/scicomp-research-skills/project-onboarding.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 4 findings, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Rogue Agent · line 77 Skill modifies its own code, configuration, or behavior at runtime. Self-modification enables an agent to escalate privileges, disable safety constraints, or install persistent backdoors.Fix: Prevent the skill from modifying its own code, SKILL.md, or configuration files. Treat skill files as read-only at runtime.
- medium Rogue Agent · line 184 Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.Fix: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
- medium Agent Snooping · line 234 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 261 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
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 5.1 | $0.00220 | $0.03988 |
| Opus 5.5 | $0.00088 | $0.01595 |
| Sonnet 5.5 | $0.00044 | $0.00798 |
| Haiku 4.5 | $0.00022 | $0.00399 |
Grade A, and why
project-onboarding 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 22d 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 — 360 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Project Onboarding (Adopting on an Existing Project)
How this skill is organised (progressive disclosure)
This skill follows the same three-level progressive-disclosure pattern as the other skills in this repository:
- Level 1 (always in context once loaded): this
SKILL.md, ~250 lines. Decision tree + universal rules + which references to load for which scenario. - Level 2 (loaded on demand by name): per-scenario reference files
in
references/, with worked examples. - Level 3 (planned future work): an interactive
bin/onboard.shhelper that automates the inventory step. Specification deferred; ad-hoc execution via the skill's reference files is sufficient while we accumulate experience.
When to load this skill
Load this skill when the user says any of:
- "I have an existing project; help me start using scicomp-research-skills on it."
- "Migrate this repo to use the scicomp-research-skills framework."
- "I already have a
CLAUDE.md/.cursorrules/AGENTS.md; how do I integrate it with this framework?" - "Adopt these skills on my existing paper / library / analysis repo."
- "Bootstrap on top of what I already have."
Auto-load trigger (added 2026-05-17 from real-project feedback): also load this skill on the FIRST tool call into a directory when ALL of:
- The current working directory contains no
AGENTS.mdat the repo root. - The canonical framework checkout (
~/.scicomp-research-skills/) exists on this machine. - The directory's contents look like a research project: presence of
any one of
*.tex,*.bib,references/,experiments/,figures/,notes/,pyproject.toml,setup.py,Project.toml,CMakeLists.txt,slides/,paper/,drafts/, OR a*.pdfin the repo root that looks like a manuscript. - The agent is about to do substantive work (drafting, editing, or creating content -- not just reading).
A real onboarding session (May 2026) on a talk-deck project showed that without this auto-load
trigger, the agent goes straight to drafting content (slides.tex)
without recognising the directory as a Scenario 1.A onboarding
opportunity. The skill therefore fires too late or not at all.
What ships with it
5 files beside SKILL.md 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.
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.
- 22d ago Changed · +3 lines · +220 tokens per session b638f139a2ba
- 2mo ago First seen · 357 lines · 0 tokens per session scan A ec081e85f3a3
project-onboarding is a skill published in the GitHub repository a-attia/scicomp-research-skills (13 stars, last pushed 23d ago), licensed MIT. It adds 220 tokens to every session and 3,988 once invoked, about $0.0009 per session on Opus 5.5. 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 2026-08-30.
project-onboarding compared with skills from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| project-onboardinga-attia/scicomp-research-skills | Skill | 13 | 23d ago | MIT | A | 220 | Claude Code, Codex |
| instrument-data-to-allotropeanthropics/knowledge-work-plugins | Skill | 35k | 2d ago | Apache-2.0 | A | 123 | Claude Code |
| exploratory-data-analysisK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 83 | Claude Code |
| matlabK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 44 | Claude Code |
| phylogeneticsK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 71 | Claude Code, Codex |
| research-engineerdavila7/claude-code-templates | Skill | 33k | yesterday | MIT | A | 43 | Claude Code, Codex |
| mapping-to-snomedmaziyarpanahi/openmed | Skill | 5.8k | yesterday | Apache-2.0 | A | 205 | Claude Code |