python "$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

rm -rf "$HOME/.codex/skills/academic-research-suite"
python "$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

/skills

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

Use $academic-research-suite.

Goal: write a journal article on AI in higher education QA
Current materials: literature matrix and rough findings, no outline yet
Output needed: paper architecture and evidence checklist
Constraints: English, APA 7, policy audience

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

/ars-plan my paper on AI governance

Use $academic-research-suite.

I want to write about AI adoption in higher education quality assurance.
I don't have a clear research question yet.
Use Socratic dialogue to help me narrow the question first.

Use $academic-research-suite.

Task: Turn these research notes into an IMRaD paper.
Materials: [attach notes.md, data_summary.csv]
Target: 6000-8000 words, APA 7, submit to Higher Education Research
Output: Full outline with section word counts, then draft intro

Use $academic-research-suite to review this manuscript.

Mode: full review
Focus: methodology, contribution, citation integrity, desk-reject risks
Output: reviewer reports + editorial decision letter

[attach manuscript.pdf or manuscript.md]

Use $academic-research-suite to start an academic-pipeline run.

Begin with Stage 0 intake and stop after producing the pipeline dashboard.
Wait for my approval before Stage 1.

Use $academic-research-suite experiment-agent.

Plan a code experiment comparing three ML models on education dataset.
Requirements: reproducible, statistical rigor, version control, artifact storage
Output: experiment protocol + reproducibility checklist

export ARS_CROSS_MODEL=claude-opus-4.7
export ANTHROPIC_API_KEY=your_api_key_here

{
  "artifact_id": "paper_v1_outline",
  "created": "2026-05-17T10:30:00Z",
  "workflow": "academic-paper",
  "stage": "outline",
  "integrity_checks": ["citation_format", "structure"],
  "sources": ["source1.pdf", "source2.pdf"],
  "status": "approved"
}

Use $academic-research-suite: ars-citation-check

[paste paper text with citations]

Verify all citations are formatted correctly in APA 7.
Flag any unverifiable sources.

Use $academic-research-suite: ars-lit-review

Topic: AI ethics in higher education
Scope: 2020-2026, peer-reviewed only
Output: thematic synthesis with citation matrix

Use $academic-research-suite: ars-format-convert

Input: [attach paper.md]
From: Markdown
To: LaTeX (IEEE conference template)
Preserve: citations, figures, tables

Use $academic-research-suite: ars-disclosure

Paper stage: final draft before submission
AI tools used: Codex for literature search, outline generation, citation formatting
Human contribution: research design, analysis, interpretation, revision
Output: journal-ready disclosure statement

Use $academic-research-suite: ars-revision-coach

[attach draft.md and reviewer_comments.txt]

Analyze reviewer feedback and suggest revision strategy.
Prioritize major vs minor revisions.
Do not rewrite yet - provide plan only.

Use $academic-research-suite: ars-revision

[attach draft.md and reviewer_comments.txt]

Execute revisions based on Reviewer 2 methodology concerns.
Track changes: show original -> revised for each section.
Update Material Passport with revision metadata.

# Remove all ARS skills
rm -rf "$HOME/.codex/skills/academic-"*
rm -rf "$HOME/.codex/skills/deep-research"
rm -rf "$HOME/.codex/skills/experiment-agent"

# Reinstall single suite
python "$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

Use $academic-research-suite deep-research workflow in socratic mode.

[your request]

Use $academic-research-suite: ars-outline

[your request]

Use $academic-research-suite academic-pipeline workflow.

Stage 0: Intake and dashboard
STOP and show dashboard for approval

[After approval]

Stage 1: Research question refinement via Socratic dialogue
STOP and show refined question

[Continue stage by stage]

Use $academic-research-suite deep-research workflow.

Search strategy: parallel tracks
Track 1: Scopus, Web of Science - quantitative studies
Track 2: Google Scholar - grey literature, policy docs
Track 3: Specialized databases - ERIC, ProQuest Education

Synthesize results into single literature matrix.

Use $academic-research-suite academic-paper-reviewer workflow.

Pass 1: Structure and contribution (desk-reject check)
[Wait for my review]

Pass 2: Methodology rigor
[Wait for my review]

Pass 3: Citation integrity and ethics
[Final decision]

Use $academic-research-suite: ars-citation-check

Citation library: Zotero export attached (bibtex format)
Paper: [attach draft.md]

Cross-check all in-text citations against Zotero library.
Flag missing entries and formatting errors.

Use $academic-research-suite experiment-agent workflow.

Existing analysis: [attach analysis.py, results.csv]
Task: Create reproducible experiment protocol around this analysis
Output: protocol.md, requirements.txt, reproduction checklist

Use $academic-research-suite: ars-format-convert

Input: [attach paper.md]
Template: University PhD thesis LaTeX template [attach template.tex]
Preserve: custom environments for theorems, university citation style

codex exec --ephemeral --sandbox read-only \
  -C /path/to/academic-research-skills-codex \
  'Use $academic-research-suite. Router smoke test only. Classify workflow and mode for: I want to write a paper on AI adoption but do not have a research question yet.'