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:

bash
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:

bash
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.

bash
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.