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Setup: Codex CLI

Prerequisites

Install

git clone https://github.com/yha9806/academic-writing-toolkit.git my-thesis
cd my-thesis
codex

Skills are loaded from .agents/skills/ (symlinked to .claude/skills/).

Setup

After cloning, run:

make setup

This sets git config core.fileMode false (avoids mode-bit noise commits), regenerates AGENTS.md / GEMINI.md from CLAUDE.md, and runs make doctor to verify the environment.

If make doctor reports anything red, run make repair to fix what it can.

Verify

Ask Codex: "What skills are available?"

You should see the public local agent skills listed in the skills guide, including evidence-review and release-governance.

Available Skills

Skill Purpose
read Guided reading with page-by-page PDF extraction
note Record structured reading notes
verify Fact-check claims against sources
map View literature coverage matrix
evidence-review Build evidence-controlled gap maps and claim registers
integrate Weave reading notes into chapter drafts
audit Pre-submission consistency check
release-governance Prepare release, rebuttal, artifact, and claim packets
style Check British English consistency
logic-review Review paragraph flow and transitions
verify-refs Check BibTeX records and metadata
progress Writing progress dashboard
export Export chapters to Word (.docx) and ZIP

Configuration

Codex reads AGENTS.md as its project instruction file, but AGENTS.md is auto-generated from CLAUDE.md (the canonical config). Edit CLAUDE.md to set your:

  • Word count targets per chapter
  • Reading pace limits
  • Directory paths for literature and chapters

Then run make sync to regenerate AGENTS.md from your changes.

Skill Invocation

Codex CLI may use different syntax for invoking skills. Check the Codex documentation for whether skills are invoked as /skill-name, $skill-name, or by natural language reference.

The skill definitions in .agents/skills/*/SKILL.md are plain Markdown and compatible with any agent that reads instruction files.

Usage Examples

read literature/my-paper.pdf         # Start reading a paper
note                                  # Record notes from reading
verify Smith published the article in 2020  # Fact-check a claim
map                                   # See literature coverage matrix
evidence-review                       # Build evidence-controlled review maps
integrate                             # Weave notes into chapters
audit                                 # Pre-submission consistency check
release-governance                    # Prepare release evidence packet
style                                 # Check British English consistency
logic-review                          # Review paragraph flow
verify-refs references.bib            # Check BibTeX records
progress                              # View writing dashboard
export chapters en-only              # Export chapters to Word