/tools

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:** 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

**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.