academic-research-skills-codex

ARS-Codex

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ARS-Codex is the Codex-native sibling of Academic Research Skills (ARS) for Claude Code. It is a separate Codex distribution with its own plugin identity, packaging, and runtime adapter. Its release number follows the vendored ARS suite.

This repository vendors the ARS workflow content as a single Codex skill:

skills/academic-research-suite/
  SKILL.md
  manifest.json
  agents/openai.yaml
  codex/
    full-runtime-manifest.json
    agents/
    hooks/
    scripts/
  ars/
    deep-research/
    academic-paper/
    academic-paper-reviewer/
    academic-pipeline/
    experiment-agent/
    commands/
    hooks/
    docs/
    tests/
    shared/

The original Claude Code ARS checkout is not modified. Upstream content is copied from fresh GitHub clones and adapted through the Codex router in skills/academic-research-suite/SKILL.md.

Relationship to Claude Code ARS

This repository is ARS-Codex. For the original Claude Code ARS distribution, use Imbad0202/academic-research-skills.

Use the Claude Code repo when you want the native Claude Code skill layout, Claude-specific agent-team behavior, or the original ARS development history. Use this repo when you want the Codex-native single-suite skill.

Versioning

This ARS-Codex package is version 3.22.0. The repo-root VERSION file, skills/academic-research-suite/SKILL.md metadata version, and skills/academic-research-suite/manifest.json adapter_version track the Codex package version in step with the vendored ARS suite, starting at 3.22.0. Earlier 0.1.x release numbers remain historical. The exact upstream version, tag, and commit are recorded in manifest.source_repositories[].

Package-level changes are summarized in CHANGELOG.md.

The vendored ARS source tracks v3.22.0 at Imbad0202/academic-research-skills@3c546bc08c56f79e0068f1ea4f0acedf5bf69b5e. This release adds the output-language-pair contract, Spanish intent routing, reviewer-calibration and plugin evaluation fixtures, and Windows file-lock repairs. It adopts upstream model-transport and audit-provenance fixes while preserving the Codex runtime and consent contracts. The output-language-pair registry currently supports only zh-tw-en; Spanish triggers do not install a Spanish output-locale pack. Claude plugin eval suites are reference material, not evidence of measured Codex performance. Nested upstream .github/ workflows and root agents/ mirrors are preserved for traceability and self-tests, but are not repo-level CI or Codex entrypoints; Claude/plugin loader files under .claude/ and .claude-plugin/ remain intentionally excluded.

Models and execution

This checkout's project configuration selects gpt-6-astra with xhigh reasoning for new trusted Codex sessions. Installing the skill does not copy that project setting or change an already-running session. The planner suggests medium for routine work and xhigh for complex work; these are starting policies, not measured optimal settings. ultra is optional in Codex for explicitly chosen demanding work and is rejected by the contained citation transport.

Native adaptive execution is the default: use bounded subagents for independent work when useful and let the lead continue with other work. The fixed full-runtime topology and hooks remain opt-in. Read the model runtime policy and system-card alignment audit.

Install ARS-Codex Plugin

Add the GitHub marketplace and install ARS-Codex with Codex CLI:

codex plugin marketplace add Imbad0202/academic-research-skills-codex --ref main
codex plugin add ars-codex@ars-codex

To update a plugin install later:

codex plugin marketplace upgrade ars-codex
codex plugin add ars-codex@ars-codex

In Codex Desktop, you can alternatively add the repository from Plugins and then install ARS-Codex:

Marketplace source: https://github.com/Imbad0202/academic-research-skills-codex.git
Branch/ref: main
Plugin: ars-codex

The plugin root is plugins/ars-codex/. Its skills/ directory contains a materialized copy of academic-research-suite, not a symlink. This keeps Codex Desktop installs portable on Windows, where plugin caches may materialize symlinks as plain text files and skip bundled skill registration.

Open a new Codex conversation after installation, then invoke $academic-research-suite or describe an academic research task that matches the bundled workflow.

Direct Skill Install Or Update

As an alternative to the plugin, install the skill directly from this repo path. Use --method git so public and credentialed GitHub access both work consistently:

python3 "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

On macOS and many Linux systems, Python 3 is exposed as python3 rather than python. If your system only has a python command and it is Python 3, use python in the commands instead.

To update an existing install:

rm -rf "$HOME/.codex/skills/academic-research-suite"
python3 "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

Open a new Codex conversation after installation. Existing Codex sessions may keep their old skill cache; you do not need to close unrelated Claude or Codex sessions.

Verify with /skills: you should see one ARS-Codex entry, academic-research-suite or ARS-Codex. You should not see separate academic-paper, academic-pipeline, deep-research, or academic-paper-reviewer skills from this package. If you do, reinstall with the update command above and open a new Codex conversation.

Codex Docs

• Codex setup covers installation, ars-* aliases, optional tools, Material Passport adapters, and unsupported Claude plugin features.
• Codex architecture explains the logical ARS pipeline with the Codex runtime overlay.
• Optional full-runtime adapter documents the disabled-by-default planner, Codex agent-team templates, and hook pack.

Usage

Invoke the suite explicitly with $academic-research-suite (singular), then describe the research task and provide any source files, notes, draft text, reviewer comments, or output constraints.

Use $academic-research-suite to help me plan a systematic literature review on
AI adoption in higher education quality assurance.

The Codex adapter routes the request to one of five ARS workflows:

Workflow Use when you need Example prompt deep-research Research question refinement, literature review, systematic review, meta-analysis, fact-checking Use $academic-research-suite to build a systematic review protocol for AI in higher education QA. academic-paper Paper outline, drafting, abstract, revision, citation formatting, AI disclosure Use $academic-research-suite to turn these notes into an IMRaD paper outline and drafting plan. academic-paper-reviewer Manuscript review, simulated peer review, editorial decision, re-review Use $academic-research-suite to review this manuscript and produce a journal-style decision letter. academic-pipeline End-to-end research-to-paper workflow with integrity gates, review, revision, and final checks Use $academic-research-suite to run an end-to-end research-to-paper pipeline from topic to revised manuscript. experiment-agent Code experiment planning, human study protocol, statistical interpretation, reproducibility validation Use $academic-research-suite to plan a code experiment and define reproducibility checks.

Claude-Style Aliases

Claude Code v3.7 installs /ars-* slash commands. Codex does not have the same plugin command registry, so this package emulates the command intent inside the single $academic-research-suite skill. Use either form:

Use $academic-research-suite: ars-plan my paper on AI governance in universities.

or, when your Codex client passes slash-prefixed text through as a normal user message:

/ars-plan my paper on AI governance in universities.

If slash input is intercepted by the client, use the plain alias form:

ars-plan my paper on AI governance in universities.

Claude command Codex alias Routed workflow /ars-plan ars-plan academic-paper plan mode /ars-outline ars-outline academic-paper outline-only mode /ars-abstract ars-abstract academic-paper abstract-only mode /ars-lit-review ars-lit-review academic-paper lit-review mode /ars-citation-check ars-citation-check academic-paper citation-check mode /ars-disclosure ars-disclosure academic-paper disclosure mode /ars-format-convert ars-format-convert academic-paper format-convert mode /ars-revision-coach ars-revision-coach academic-paper revision-coach mode /ars-revision ars-revision academic-paper revision mode /ars-reviewer ars-reviewer academic-paper-reviewer full mode /ars-mark-read ars-mark-read Human-read signal for citation keys in the active Material Passport /ars-unmark-read ars-unmark-read Rescind a prior human-read signal /ars-cache-invalidate ars-cache-invalidate Invalidate cached verification entries for one citation key /ars-full ars-full academic-pipeline full workflow

Working Pattern

For best results, start with the workflow goal and the current state of your materials:

Use $academic-research-suite.

Goal: write a journal article.
Current materials: I have a literature matrix and rough findings, but no outline.
Output needed now: paper architecture and missing-evidence checklist.
Constraints: English, APA 7, higher education policy audience.

If you only have a paper topic or broad research direction and do not yet have a clear research question, the Codex router should start with ARS Socratic scoping:

Use $academic-research-suite.

I want to write a paper on AI adoption in higher education quality assurance.
I do not yet have a clear research question.
Please use SCR / Socratic dialogue to help me narrow the question first; do not write an outline yet.

Expected route: deep-research socratic mode first. ARS should ask narrowing questions and should not produce an outline or draft until the research question has converged.

For review tasks, provide the manuscript or a path to the manuscript, plus the review mode you want:

Use $academic-research-suite to review this paper.
Mode: full review.
Focus: methodology, contribution, citation integrity, and likely desk-reject risks.
Output: reviewer reports plus editorial decision letter.

For staged pipelines, ask for a checkpoint instead of asking Codex to run the entire process silently:

Use $academic-research-suite to start an academic-pipeline run.
Begin with Stage 0 intake and stop after producing the pipeline dashboard.

Smoke Tests

In a new Codex conversation:

/skills

Expected: one ARS entry only.

Then test Socratic routing:

Use $academic-research-suite.
I want to write a paper on