.gitignore

# ==============================================================================
# .gitignore for Academic Claude Code Projects
# ==============================================================================

# LaTeX build artifacts
*.aux
*.bbl
*.blg
*.fdb_latexmk
*.fls
*.log
*.nav
*.out
*.snm
*.toc
*.vrb
*.synctex.gz
*.run.xml
*-blx.bib

# Compiled PDFs (uncomment to track specific PDFs)
# *.pdf

# Python
__pycache__/
*.pyc
*.pyo

# R
.Rproj.user/
.Rhistory
.RData
.Rdata

# OS files
.DS_Store
Thumbs.db

# Claude Code local files (not shared across machines)
.claude/settings.local.json
.claude/state/
CLAUDE.local.md

# IDE
# .vscode/settings.json ships in the template (carries shipped Claude Code permission-mode
# recommendations — see TROUBLESHOOTING.md "Permissions / bypass / statusline" for the typo
# fix forkers need). Other .vscode/ content is developer-machine-specific.
.vscode/*
!.vscode/settings.json
.idea/
*.swp
*.swo
*~

# Quarto rendering artifacts
.quarto/

# quality_reports/ — per-project session logs, plans, specs, merges, audits,
# diagnoses. The directory structure ships in the template (via .gitkeep), but
# the content is PROJECT-INTERNAL and shouldn't be inherited by forks.
# (diagnoses/ in particular may hold real data values/paths — never ship them;
#  audits/ are repo-specific gap analyses, noise for a forker.)
quality_reports/plans/*
quality_reports/specs/*
quality_reports/session_logs/*
quality_reports/merges/*
quality_reports/decisions/*
quality_reports/checkpoints/*
quality_reports/preregistrations/*
quality_reports/audits/*
quality_reports/diagnoses/*
!quality_reports/plans/.gitkeep
!quality_reports/specs/.gitkeep
!quality_reports/session_logs/.gitkeep
!quality_reports/merges/.gitkeep
!quality_reports/decisions/.gitkeep
!quality_reports/checkpoints/.gitkeep
!quality_reports/preregistrations/.gitkeep
!quality_reports/audits/.gitkeep
!quality_reports/diagnoses/.gitkeep

# R analysis outputs (generated artifacts; keep scripts, ignore outputs)
scripts/R/_outputs/

# Output artifacts — uncomment lines below based on your preference
# *.rds
# output/**/*.rds