tools

name	tools
description	Utility workflows for compile, bibliography validation, journal/log inspection, runtime smoke tests, memory updates, bootstrap tasks, and infrastructure refresh. Use when the user asks for mechanical project maintenance rather than substantive research work.

Tools

Run lightweight utility workflows for project maintenance and infrastructure.

Read First

• AGENTS.md
• plugins/clo-author/references/runtime-activation.md
• plugins/clo-author/references/codex-workflow.md
• plugins/clo-author/references/logging.md
• MEMORY.md when the task concerns durable learnings

Supported Subroutines

• commit preparation
• compile
• validate bibliography
• journal timeline summary
• context summary
• deploy docs
• learn
• runtime activation smoke test
• bootstrap template
• upgrade infrastructure

Common Procedures

Compile

Use the active paper chain:

cd paper && TEXINPUTS=preambles:$TEXINPUTS xelatex -interaction=nonstopmode main.tex
biber main
TEXINPUTS=preambles:$TEXINPUTS xelatex -interaction=nonstopmode main.tex
TEXINPUTS=preambles:$TEXINPUTS xelatex -interaction=nonstopmode main.tex

Validate Bibliography

Cross-check \cite{} keys against Bibliography_base.bib and report:

• missing keys
• unused keys
• duplicates

Runtime Activation Smoke Test

Use plugins/clo-author/references/runtime-activation.md as the contract and report whether the session is active or blocked before claiming the plugin is available.

If the home-level skill link is missing, install or verify it with:

bash scripts/install_codex_skill_link.sh

Journal / Context Summary

Summarise the latest plan, session log, and research journal when the user asks for current state or recovery context.

Learn

When updating memory, write concise [LEARN:*] entries grounded in actual mistakes or durable workflow discoveries.

Upgrade Infrastructure

Refresh the Codex-native infrastructure selectively:

• update plugins/clo-author/skills/
• update plugins/clo-author/references/
• update templates and guide docs
• preserve user research content under paper/, scripts/, data/, quality_reports/, and MEMORY.md

Principles

• Keep these tasks lightweight.
• Prefer deterministic commands and scripts.
• Treat compile, lint, and activation checks as evidence-producing workflows.
• Never overwrite user research content during infrastructure refreshes.