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CLAUDE.MD -- Academic Project Development with Claude Code

Project: [YOUR PROJECT NAME] Institution: [YOUR INSTITUTION] Branch: main

Core Principles

  • Plan first -- enter plan mode before non-trivial tasks; save plans to quality_reports/plans/
  • Verify after -- compile/render and confirm output at the end of every task
  • Single source of truth -- Beamer .tex is authoritative; Quarto .qmd derives from it
  • Quality gates -- nothing ships below 80/100
  • [LEARN] tags -- when corrected, save [LEARN:category] wrong → right to MEMORY.md

Folder Structure

[YOUR-PROJECT]/
├── CLAUDE.MD                    # This file
├── .claude/                     # Rules, skills, agents, hooks
├── Bibliography_base.bib        # Centralized bibliography
├── Figures/                     # Figures and images
├── Preambles/header.tex         # LaTeX headers
├── Slides/                      # Beamer .tex files
├── Quarto/                      # RevealJS .qmd files + theme
├── docs/                        # GitHub Pages (auto-generated)
├── scripts/                     # Utility scripts + R code
├── quality_reports/             # Plans, session logs, merge reports
├── explorations/                # Research sandbox (see rules)
├── templates/                   # Session log, quality report templates
└── master_supporting_docs/      # Papers and existing slides

Commands

# LaTeX (3-pass, XeLaTeX only)
cd Slides && TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode file.tex
BIBINPUTS=..:$BIBINPUTS bibtex file
TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode file.tex
TEXINPUTS=../Preambles:$TEXINPUTS xelatex -interaction=nonstopmode file.tex

# Deploy Quarto to GitHub Pages
./scripts/sync_to_docs.sh LectureN

# Quality score
python scripts/quality_score.py Quarto/file.qmd

Quality Thresholds

Score Gate Meaning
80 Commit Good enough to save
90 PR Ready for deployment
95 Excellence Aspirational

Skills Quick Reference

Command What It Does
/compile-latex [file] 3-pass XeLaTeX + bibtex
/deploy [LectureN] Render Quarto + sync to docs/
/extract-tikz [LectureN] TikZ → PDF → SVG
/proofread [file] Grammar/typo/overflow review
/visual-audit [file] Slide layout audit
/pedagogy-review [file] Narrative, notation, pacing review
/review-r [file] R code quality review
/qa-quarto [LectureN] Adversarial Quarto vs Beamer QA
/slide-excellence [file] Combined multi-agent review
/translate-to-quarto [file] Beamer → Quarto translation
/validate-bib Cross-reference citations
/devils-advocate Challenge slide design
/create-lecture Full lecture creation
/commit [msg] Stage, commit, PR, merge
/lit-review [topic] Literature search + synthesis
/research-ideation [topic] Research questions + strategies
/interview-me [topic] Interactive research interview
/review-paper [file] Manuscript review
/data-analysis [dataset] End-to-end R analysis
/learn [skill-name] Extract discovery into persistent skill
/context-status Show session health + context usage
/deep-audit Repository-wide consistency audit

Beamer Custom Environments

Environment Effect Use Case
[your-env] [Description] [When to use]

Quarto CSS Classes

Class Effect Use Case
[.your-class] [Description] [When to use]

Current Project State

Lecture Beamer Quarto Key Content
1: [Topic] Lecture01_Topic.tex Lecture1_Topic.qmd [Brief description]
2: [Topic] Lecture02_Topic.tex -- [Brief description]