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Agent skill

Tools

by brycewang-stanford in brycewang-stanford/Auto-Empirical-Research-Skills

Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn.

Custom licenceAuto-check: notesDevelopment

Install Tools

skills CLI
$ npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill tools -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install brycewang-stanford/Auto-Empirical-Research-Skills tools --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/16-hsantanna88-clo-author/dot-claude/skills/tools .claude/skills/tools && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
tools
GitHub stars
4.5k
Token cost
~1k tokens
SKILL.md length
299 words
Files
1
Skills in repo
369
Repo updated
First seen
Licence
Custom licence

At a glance

Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn.

  • Works in 7 steps: Clone the latest clo-author release into… → Save the user's filled-in… → Delete the old .claude/ directory → …
  • Tasks that involve Citation management
  • SKILL.md covers Subcommands and Principles
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Tools is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn. Replaces individual utility skills.

Its SKILL.md is about 1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Development, covering Citation management and Commit messages. It works with LaTeX. The repository describes itself as: 🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. | 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI…

When your agent uses it

  • Tasks that involve Citation management
  • Tasks that involve Commit messages

Example prompts

  • “/tools”

Requirements

  • Pre-approved tools (allowed-tools): Read, Grep, Glob, Write, Edit, Bash, Task

Workflow steps

7 steps, taken from the first numbered list in SKILL.md.

  1. Clone the latest clo-author release into a temp directory
  2. Save the user's filled-in domain-profile.md and any custom journal profiles
  3. Delete the old .claude/ directory
  4. Copy the new .claude/ in
  5. Restore the user's domain-profile.md and custom journal profiles
  6. Optionally copy new templates/
  7. Report what changed

What it can do on your machine

Read from SKILL.md and the folder at commit 9fa87d8. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves these tools, so the agent can use them without asking each time:

    • Read
    • Grep
    • Glob
    • Write
    • Edit
    • Bash
    • Task

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are bash).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Tools loads about 1k tokens when it runs. Until then it costs about 33 tokens; SKILL.md has 299 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~33
When it runs · the whole SKILL.md, loaded when a task matches
~1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check: notes

The automated check noted patterns worth knowing about, such as sudo or a known installer.

  • NoteMentions a .env fileSKILL.md:21
    - Stage relevant files (never stage .env or credentials)
  • NotePre-approves every shell command (allowed-tools: Bash)SKILL.md
    allowed-tools: Read, Grep, Glob, Write, Edit, Bash, Task

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 299 words (~1,017 tokens).

“Utility subcommands for project maintenance and infrastructure.”

— opening of SKILL.md by brycewang-stanford, Custom licence
name
tools
allowed-tools
Read, Grep, Glob, Write, Edit, Bash, Task
argument-hint
[subcommand: commit | compile | validate-bib | journal | context | deploy | learn | upgrade] [args]

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/16-hsantanna88-clo-author/dot-claude/skills/tools of brycewang-stanford/Auto-Empirical-Research-Skills.

Open the folder on GitHubat commit 9fa87d8

Compare with similar skills

Tools next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Tools compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tools this skillbrycewang-stanford/Auto-Empirical-Research-Skills4.5k—~1kAutomated safety check: NotesCustom licence
Collaborating With Geminiappautomaton/latex-arxiv-SKILL4571 repos~1.1kAutomated safety check: PassMIT
Git Workflowsoftmaple/softmaple159—~814Automated safety check: PassApache-2.0
Release ExtensionYorick-Ryu/deep-share144—~1.3kAutomated safety check: PassCustom licence
Collaborating With Claudeappautomaton/latex-arxiv-SKILL4571 repos~1.5kAutomated safety check: PassMIT
Citation Managementneflibata-feng/MyArxiv-Agent12620 repos~8.1kAutomated safety check: NotesMIT

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Works with

Categories

Questions about Tools

What does Tools do?

Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn. Tools is an agent skill from brycewang-stanford/Auto-Empirical-Research-Skills. Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn.

When should I use Tools?

Tools fits situations like: tasks that involve Citation management; tasks that involve Commit messages.

How do I install Tools in Claude Code?

Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill tools -a claude-code`. Or copy the skill folder (skills/16-hsantanna88-clo-author/dot-claude/skills/tools in brycewang-stanford/Auto-Empirical-Research-Skills) into .claude/skills/tools in your project. Claude Code loads it when a task matches its description.

How do I install Tools in Codex?

Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill tools -a codex`. Or copy the skill folder (skills/16-hsantanna88-clo-author/dot-claude/skills/tools in brycewang-stanford/Auto-Empirical-Research-Skills) into .agents/skills/tools in your project. Codex loads it when a task matches its description.

Can I use Tools in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill tools -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tools, .gemini/skills/tools, .github/skills/tools and .opencode/skills/tools in your project.

What does Tools need to run?

SKILL.md names no scripts, command-line tools or credentials: Tools is instructions for the agent only. Its frontmatter pre-approves these tools: Read, Grep, Glob, Write, Edit, Bash, Task.

Does Tools access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Tools safe to install?

Our automated static check of SKILL.md found notes only (mentions a .env file; pre-approves every shell command (allowed-tools: bash)), nothing it rates as a warning. It is not a guarantee. Review the folder before installing.

What licence does Tools use?

Tools has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.

How many tokens does Tools use?

About 1k tokens (SKILL.md is roughly 4.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Tools?

Skills that share tags, products or a category with Tools: Collaborating With Gemini (appautomaton/latex-arxiv-SKILL, 457 stars), Git Workflow (softmaple/softmaple, 159 stars), Release Extension (Yorick-Ryu/deep-share, 144 stars) and Collaborating With Claude (appautomaton/latex-arxiv-SKILL, 457 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tools?

brycewang-stanford (a GitHub user) maintains it in brycewang-stanford/Auto-Empirical-Research-Skills, which has 4,517 GitHub stars. The repository holds 369 skills in this directory. The repository was last updated on October 5, 2026.

Source: brycewang-stanford/Auto-Empirical-Research-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.