brycewang-stanford/tools
skills/16-hsantanna88-clo-author/dot-claude/skills/tools/SKILL.md
Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn. Replaces individual utility skills.
$ install --global
skillsauthnpx skillsauth add brycewang-stanford/Awesome-Agent-Skills-for-Empirical-Research toolsInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- tools
- description:
- Utility commands — commit, compile, validate-bib, journal, context-status, deploy, learn. Replaces individual utility skills.
- argument-hint:
- [subcommand: commit | compile | validate-bib | journal | context | deploy | learn | upgrade] [args]
- allowed-tools:
- Read,Grep,Glob,Write,Edit,Bash,Task
Tools
Utility subcommands for project maintenance and infrastructure.
Input: $ARGUMENTS — subcommand followed by any arguments.
Subcommands
/tools commit [message] — Git Commit
Stage changes, create commit, optionally create PR and merge.
- Run git status to identify changes
- Stage relevant files (never stage .env or credentials)
- Create commit with descriptive message
- If quality score available and >= 80, note in commit
/tools compile [file] — LaTeX Compilation
3-pass XeLaTeX + bibtex compilation.
For papers:
cd Paper && TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode [file]
BIBINPUTS=..:$BIBINPUTS bibtex [file_base]
TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode [file]
TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode [file]
For talks:
cd Talks && TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode [file]
/tools validate-bib — Bibliography Validation
Cross-reference all \cite{} keys in paper and talk files against Bibliography_base.bib. Report: missing entries, unused entries, duplicate keys.
/tools journal — Research Journal
Regenerate the research journal timeline from quality reports and git history. Shows chronological record of agent actions, phase transitions, scores, decisions.
/tools context — Context Status
Show current context status and session health. Check context usage, whether auto-compact is approaching, what state will be preserved.
/tools deploy — Deploy Guide Site
Render Quarto guide site and publish to GitHub Pages.
cd guide && quarto publish gh-pages --no-browser
/tools learn — Extract Learnings
Extract reusable knowledge from the current session. Auto-memory handles corrections automatically; this is for multi-step workflows worth turning into a full skill.
/tools upgrade — Upgrade Clo-Author Infrastructure
Upgrade an existing project to the latest clo-author architecture.
What it does:
- Clone the latest clo-author release into a temp directory
- Save the user's filled-in domain-profile.md and any custom journal profiles
- Delete the old
.claude/directory - Copy the new
.claude/in - Restore the user's domain-profile.md and custom journal profiles
- Optionally copy new
templates/ - Report what changed
Workflow:
Step 1: DOWNLOAD
- Clone latest clo-author into /tmp/clo-author-upgrade
- Or: gh release download --repo hugosantanna/clo-author
Step 2: PRESERVE USER CUSTOMIZATIONS
- Save .claude/references/domain-profile.md if filled in (not just placeholders)
- Save any custom journal profiles the user added to journal-profiles.md
- Save .claude/settings.json (user's permissions and hooks)
- Save .claude/settings.local.json if it exists
Step 3: REPLACE
- Delete old .claude/ entirely
- Copy new .claude/ from the downloaded release
- Restore saved customizations from Step 2
Step 4: DO NOT TOUCH
- paper/, scripts/, data/, explorations/, quality_reports/
- CLAUDE.md, Bibliography_base.bib, README.md, .gitignore
- Any other user content
Step 5: REPORT
- List what was updated (new agents, skills, rules)
- List what was preserved (domain profile, settings, custom profiles)
- Clean up temp directory
No git merge. No upstream remote. No conflicts. Just delete and replace .claude/.
Principles
- Each subcommand is lightweight. No multi-agent orchestration needed.
- Compile always uses 3-pass. Ensures references and citations resolve.
- validate-bib catches drift. Run before commits to catch broken citations.
- Upgrade preserves content. Infrastructure changes, your paper doesn't.
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