What is using-git-and-github?

A guide to using Git, a version-control system, and GitHub, a service for hosting and collaborating on Git repositories, in research projects.

Use it when creating commits or branches, deciding what to track or ignore, pushing from an HPC cluster, or opening pull requests.

It helps decide what belongs in version control, keeps commits understandable, and avoids exposing secrets or filling repositories with large generated files.

using-git-and-github — Skill for Claude Code by yale-som-hpc

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.

Any agent

npx skills add yale-som-hpc/claude-code-marketplace --skill using-git-and-github

Clone the repo

git clone --depth 1 https://github.com/yale-som-hpc/claude-code-marketplace

Made for: Claude Code.

Or install hpc, the plugin that ships this one along with the rest of its 23 skills, 3 commands.

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github/github.svg)](https://agentmods.dev/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github)

Your own site

<a href="https://agentmods.dev/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github"><img src="https://agentmods.dev/badge/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github"><img src="https://agentmods.dev/badge/skills/yale-som-hpc/claude-code-marketplace/using-git-and-github.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 68 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,101 The whole file, excluding the scripts and references it only reads on demand.

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.

Token cost

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	$0.00068	$0.01101
Opus 5.5	$0.00027	$0.00440
Sonnet 5.5	$0.00014	$0.00220
Haiku 4.5	$0.00007	$0.00110

Measured 2mo ago against content hash b7e6a38046c4, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

using-git-and-github 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 2mo 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.

plugins/hpc/skills/using-git-and-github/SKILL.md · 185 lines

How it starts

The opening of the file, as written. The whole thing — 185 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Using Git and GitHub

For agents helping researchers get version-control benefits without becoming git experts.

Rules

Track code, config, metadata, docs, lockfiles, small examples.
Do not track raw data, secrets, env dirs, package libraries, large generated outputs.
Commit logical checkpoints.
Prefer simple history. No force-push on shared branches unless explicitly approved.
Explain git decisions plainly.

Git on HPC

Git may require a module:

module load git
git --version

Use module load git in setup notes/scripts that need git on HPC.

Auth and pushing

Laptop: HTTPS with gh auth login or normal SSH keys are fine.

HPC: prefer SSH agent forwarding so private keys stay on the laptop:

ssh -A hpc
module load git
ssh -T [email protected]
git push

If SSH_AUTH_SOCK is stale, fix the socket pointer. Do not copy private keys to the cluster. See connecting securely.

HTTPS / gh token auth is also fine if already configured:

module load git
gh auth status
git push

Never copy ~/.ssh/id_* private keys onto the cluster. Public keys (*.pub) are safe; private keys are not.

Agent behavior

Run git status --short before and after edits.
Do not silently stage ambiguous untracked files. Report and propose track/ignore/refuse.
Commit when asked, or when a coherent requested task is complete and repo norms expect commits. If uncertain, ask once.
Use imperative messages: Add panel construction script, Fix Slurm memory request.
Report hash + summary.

Track / ignore

Track:

source, scripts, Slurm scripts,
README/docs,
pyproject.toml, uv.lock, renv.lock, .Rprofile,
small metadata/codebooks/config,
tiny synthetic fixtures,
Makefiles/justfiles.

Ignore:

# Data and outputs
data/raw/
data/derived/
output/
outputs/
results/
logs/
*.parquet
*.rds
*.RDS
*.dta
*.sas7bdat
*.feather
*.h5
*.h5ad

# Python
.venv/
__pycache__/
*.pyc
.pytest_cache/
.ruff_cache/

# R
.Rhistory
.RData
.Rproj.user/
renv/library/
renv/local/
renv/staging/

# Secrets / local config
.env
.env.local
*.pem
*.key

# OS/editor
.DS_Store
Thumbs.db

Read the full file on GitHub · 185 lines

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.

2mo ago First seen · 185 lines · 68 tokens per session scan A b7e6a38046c4

Subscribe to this mod's changes

using-git-and-github is a skill published in the GitHub repository yale-som-hpc/claude-code-marketplace (5 stars, last pushed 3mo ago), licensed Unlicense. It adds 68 tokens to every session and 1,101 once invoked, about $0.0003 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 2026-08-31.

Commits Git and workflow Research

using-git-and-github next to 6 skills from other repositories
Mod	Type	Stars	Last push	Licence	Scan	Tokens	Works with
using-git-and-githubyale-som-hpc/claude-code-marketplace	Skill	5	3mo ago	Unlicense	A	68	Claude Code
create-prprisma/orm	Skill	48k	yesterday	Apache-2.0	A	48	Claude Code, Codex
git-commitThinkInAIXYZ/deepchat	Skill	6.4k	yesterday	Apache-2.0	A	15	Claude Code, Codex
repo-syncdavidondrej/skills	Skill	4.3k	3d ago	MIT	A	25	Claude Code, Codex
engineer-bot-opsmakecindy/cindy	Skill	9.3k	yesterday	Apache-2.0	A	57	Claude Code, Codex
mcore-split-prNVIDIA/skills	Skill	3.9k	yesterday	Apache-2.0	A	25	Claude Code
git-commit-writermergisi/awesome-openclaw-agents	Skill	4.1k	2d ago	MIT	A	53	Claude Code, Codex