Homogenize repository configuration

- sync the common .gitignore base (computorg/.github gitignore/computo.gitignore)
- version renv auto-loaders (.Rprofile, renv/activate.R), as recommended by renv
- untrack files that should never have been versioned (logo_text_white.pdf)

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

Author: jchiquet

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.gitignore

@@ -1,49 +1,74 @@
-# R and co
-.Rhistory
-.Rprofile
-.Rapp.history
-.RData
-.Ruserdata
-*.Rproj
-.Rproj.user
-.Rproj.user/
-/*.Rcheck/
-renv/
-
-# Python and co
-_environment
-/.micromamba/
-/.joblib
-/.pytest_cache/
-scripts/__pycache__/
-
-# Quarto tmp files
-/.quarto/
-/*_files
-/*_cache
-/_freeze
-_site/
-/cache/
+# >>> computorg base (managed by tools-automation/sync-gitignore.py, do not edit) >>>
+# Common base for Computo article and template repositories.
+# Synced into each repository's .gitignore between the "computorg base" markers;
+# add repository-specific entries below the closing marker.
 
-# Quarto extension files
-_extensions/
-logo_text_white.pdf
-logo_notext_white.png
+# Quarto
+.quarto/
+/_site/
+/_freeze/
+**/*.quarto_ipynb
+.luarc.json
 
-# Quarto output files
-main.pdf
-main.html
-main.ipynb
-main.tex
+# Computo extension: installed on the fly by CI, never versioned
+/_extensions/
+/logo_text_white.pdf
+/logo_notext_white.png
 
-# Latex compilation files
+# Rendered outputs of the source documents (main.qmd, README.qmd, template-computo-*.qmd)
+/main.html
+/main.pdf
+/main.tex
+/main.ipynb
+/main_files/
+/main_cache/
+/README.html
+/README_files/
+/template-computo-*.html
+/template-computo-*.pdf
+/template-computo-*.tex
+/template-computo-*.ipynb
+/template-computo-*_files/
+/template-computo-*_cache/
+# legacy source documents named after the repository
+/published-*.html
+/published-*.pdf
+/published-*.tex
+/published-*.ipynb
+/published-*_files/
+/published-*_cache/
 *.aux
 *.log
 *.toc
 
-# Various system files
-DS_Store
-/.luarc.json
+# R
+.Rhistory
+.Rapp.history
+.RData
+.Ruserdata
+.Rproj.user/
+*.Rproj
+*.Rcheck/
+_environment
+# renv: .Rprofile, renv.lock and renv/{activate.R,settings.json,.gitignore} ARE versioned;
+# the package library and renv working directories are not (also excluded by renv/.gitignore)
+renv/library/
+renv/local/
+renv/cellar/
+renv/lock/
+renv/python/
+renv/sandbox/
+renv/staging/
 
+# Python
+__pycache__/
+.pytest_cache/
+.micromamba/
+.joblib
+.venv/
 
-**/*.quarto_ipynb
+# Misc
+cache/
+.DS_Store
+.claude/
+# <<< computorg base <<<

logo_text_white.pdf

@@ -0,0 +1,7 @@
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/