academic-research-skills-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/
    sr-screener/
    experiment-agent/
    commands/
    hooks/
    docs/
    tests/
    shared/

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

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.

This ARS-Codex package is version 3.24.0. 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 v3.24.0 at Imbad0202/academic-research-skills@b34c63f828b3535f403079a4f42bc7955da2f64b. This release adds two advisory attachments to the Editorial Decision Letter. The suggested-reference check looks up the works that Reviewer 2 and Reviewer 3 recommend; in Codex it runs only when you ask for it, because it queries four bibliographic indexes. The reviewer claim check asks one isolated worker of the active Codex model whether the manuscript contradicts each panel finding. It is on by default, and ARS_PANEL_CLAIM_CHECK=0 turns it off. Neither attachment changes the decision or the revision roadmap, and their accuracy on real reviews is unmeasured. Integrity-rule repairs treat a prior report as fresh only when it is under 24 hours old, and a revised paper entering at Stage 5 runs Stage 4.5 first. The guard-launcher and startup-notice fixes remain inactive Claude references in Codex. There is no new workflow, and the native Codex model policy is unchanged. The output-language-pair registry still supports only zh-tw-en; Spanish triggers do not install a Spanish output-locale pack. Claude model audits and plugin eval suites are reference material and do not change the Codex model policy or establish 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.

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.

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

Windows update recovery: if failed updates repeatedly create marketplace-upgrade-* directories or fill the system drive, stop retrying and open the local marketplace recovery guide. If the drive is full, first follow its step 1 to stop Codex and free space safely. Codex CLI 0.164.0 includes upstream fixes that clean up leftover staging directories, so then check the CLI version bundled with Codex Desktop and update if it is older. If leftover directories still accumulate on 0.164.0 or later, continue with the guide: it covers preserving a working copy, switching only ARS to a local source, verification, and manual updates. After switching to a local source, use that guide's manual update procedure instead of marketplace upgrade. Disabling the plugin alone is insufficient: Codex can still refresh files for disabled configured plugins. The guide is a workaround for #43; the Windows os error 5 failure reported there has not been retested on 0.164.0.

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.

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 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.

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 six ARS workflows:

sr-screener has eight modes: protocol, quick, pilot, ta-screen, ft-screen, adjudicate, audit, and report. Screening starts only on an explicit request; deep-research systematic-review never hands off to it automatically. The review team confirms the eligibility rules and verifies AI decisions. Full title/abstract screening requires a pilot comparison with the team's labels that misses no record the team advanced, unless the user records an override. Counts remain provisional until a senior reviewer completes QC of a reproducible sample of jointly excluded records (minimum 20, default 100; all exclusions when fewer are available). Missing or malformed decisions remain pending. Synthetic tests exercise the scripts; screening accuracy has not been measured.

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.

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.

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 AI adoption in higher education quality assurance.
I do not yet have a clear research question.

Expected: route to deep-research socratic mode and ask narrowing questions.

CLI smoke test:

codex exec --ephemeral --sandbox read-only \
  -C /path/to/academic-research-skills-codex \
  'Use $academic-research-suite. Router smoke test only. User request to classify: I want to write a paper on AI adoption in higher education quality assurance, but I do not yet have a clear research question. According to the academic-research-suite router, classify the workflow and mode.'

Maintainer quality gates:

python3 skills/academic-research-suite/codex/scripts/ars_codex_quality_gates.py all --json

Expected: every reported gate has "ok": true.

These Codex messages do not mean ARS failed to install:

• [features].codex_hooks is deprecated — update your Codex config when convenient; ARS-Codex does not require hooks for normal use.
• hooks need review before they can run — review those hooks separately if you use them. ARS-Codex treats vendored Claude hooks as traceability metadata and does not require them.

ARS was originally written for Claude Code. In this Codex package:

• The vendored agents/*.md files are used as role and phase prompts.
• The Codex-only codex/ directory contains an optional full-runtime adapter profile. Its fixed topology and hook pack are opt-in; normal execution adapts native subagents to the task.
• The vendored commands/ars-*.md files are prompt recipes only. Codex does not register them as slash commands.
• The vendored hooks/hooks.json file is preserved for upstream traceability only. Codex does not install Claude Code hooks from this package.
• Codex may delegate bounded independent work through native subagents within the current task and permissions, while the lead continues useful work.
• Web/source verification uses Codex browsing and must cite sources when current or external facts matter.
• Cross-model verification is disabled by default. When explicitly requested in this Codex package, follow the vendored provider setup in ars/shared/cross_model_verification.md, identify the provider/model/content class first, and obtain explicit user consent before any external upload. External reviewers are called through configured provider APIs, not simulated through the active Codex model.
• ARS_MODEL_TIERING is unset by default. The Codex adapter preserves the upstream judgment/execution classification but applies economy or quality-boost only when the runtime supports an explicit per-dispatch model override; otherwise it reports a no-op and keeps the active model.
• Protected top-level agent tools: allowlists remain least-privilege role boundaries. A dispatched checkpoint owner does not gain Bash or network transport; the dispatching Codex context owns any explicitly consented cross-model call.
• A [CROSS-MODEL-HANDOFF v1] block is a transport request, not a deliverable. The dispatcher validates it, sends only its payload, applies the mechanical result routing, and returns judgment work to the original owner.
• In reviewer full mode, an explicitly configured and consented cross-model run swaps the existing Reviewer 2 seat; it never adds a sixth reviewer. Re-review applies the separate Priority-1 judge pass and records provenance. Single-family execution and provider fallback are disclosed.
• ARS_CACHE_STALE_ADVISORY_DAYS controls the advisory-only cache-age threshold, while ARS_CACHE_REVALIDATE=1 opts into live bibliographic re-validation. These settings apply when the programmatic citation gate is run; stale rows alone never fail an integrity gate.
• Locally read PDFs run the structural pdf_read_preflight.py by default before page anchors are trusted. FAIL and UNAVAILABLE remain distinct, and a missing parser or sidecar is never treated as PASS. The v3.20 sandboxed content classifier is an explicit opt-in advisory and cannot override this structural preflight.
• ars-mark-read requires a user-declared read_scope for every new mark. Explicit unknown and legacy scope-less records remain coverage_unknown; partial coverage stays visible and Codex never infers full-text reading.
• Revision rounds use the v3.20 evidence-bound, non-ranking roadmap and explicit author-adjudication contract. They also preserve the v3.19-introduced claim-strength ladder and deterministic numeric, citation, marker, and protected-term conservation checks as advisory-first guards.
• The upstream v3.18 SessionStart update checker is vendored but not installed or executed as a Codex hook. Plugin users update with codex plugin marketplace upgrade ars-codex followed by codex plugin add ars-codex@ars-codex; direct skill installs still update by reinstalling or pulling this repository.
• Upstream references to a "fresh Claude Code session" mean a new Codex conversation in this package; Material Passport reset semantics still apply.
• If a citation, source, statistic, or journal policy cannot be verified, Codex should mark it as unverified rather than invent support.

This package adapts upstream ARS v3.24.0 at b34c63f828b3535f403079a4f42bc7955da2f64b wherever Codex has an equivalent concept, with documented model/runtime overlays.

Bibliographic network behavior is intentionally explicit at the Codex adapter boundary:

For reviewer calibration or cross-model devil's advocate checks, configure one of the provider tuples documented in ars/shared/cross_model_verification.md, then ask for cross-model verification explicitly in the prompt. For example:

export OPENAI_API_KEY="<your-openai-api-key>"
export ARS_CROSS_MODEL="gpt-6-astra"

gpt-6-astra remains provisional on both verifier transports. A GPT verifier used by a GPT session is a separate run in the same family, not cross-family validation. Provider/content/cost consent still applies.

Without both a configured provider and explicit user consent for the content class being sent, ARS-Codex falls back to single-runtime review and reports that cross-model verification was unavailable.

If ARS-Codex helps your research workflow, you can support maintenance through Buy Me a Coffee.

Do not open public issues for vulnerabilities. Follow SECURITY.md for private reporting, and see the release readiness and security report for the latest local validation summary.

The entry point is:

skills/academic-research-suite/SKILL.md

Workflow content is under:

skills/academic-research-suite/ars/<workflow>/

Shared schemas, compliance rules, and cross-workflow contracts are under:

skills/academic-research-suite/ars/shared/

When debugging or updating the package, preserve these paths. Many ARS workflow files cross-reference shared/, scripts/, examples/, and other workflow directories.

Updates sync selected upstream ARS content into skills/academic-research-suite/ars/. Do not mirror the Claude Code repo blindly; exclude Claude/plugin loader files such as .claude/, .claude-plugin/, source .gitignore, and symlink-only alias directories that are not needed in Codex. Nested upstream .github/ workflows may be retained as inactive traceability and self-test fixtures.

Some upstream maintenance scripts are vendored but intentionally inactive in this Codex package because they require non-vendored Claude Code inputs such as .claude/CLAUDE.md. See inactive_upstream_scripts in skills/academic-research-suite/manifest.json before wiring any upstream script into Codex CI.

Cheng-I Wu - Maintainer of the ARS suite and this Codex sibling distribution.

Codex - Assisted with the Codex adapter packaging, router-policy hardening, test fixes, and release-readiness review under maintainer direction.

vinschger - Reported beginner installation friction around python vs python3, which led to clearer setup instructions for macOS and other environments.

Joker2377 - Helped answer community installation questions and clarify beginner setup steps in issue discussions.

Vendored upstream ARS contributors are acknowledged in skills/academic-research-suite/ars/README.md.