[codex] public release cleanup

[Larsvanderlaan]

What changed

• make paper/main.tex the canonical public manuscript build and sync docs/paper.pdf
• narrow the public reproduction path to the paper-backed simulation, ppi_py, toy, and PPE assets
• improve public README/reproduction instructions and add paper-specific build notes
• fix the LLM benchmark plotting bug and make the toy/LLM tests hermetic
• update GitHub Actions so R Suggests dependencies are installed before the package tests run

Why

• the repo is being prepared for a cleaner public release
• the previous push/checks flow could fail because testthat and other R dependencies were not installed in CI

Validation

• ./.venv/bin/pytest -q
• R CMD INSTALL -l /tmp/ppiAIPW-lib r/ppiAIPW
• env R_LIBS=/tmp/ppiAIPW-lib Rscript -e "library(testthat); library(ppiAIPW); testthat::test_dir('r/ppiAIPW/tests/testthat', reporter='summary')"
• ./scripts/reproduce_paper.sh --smoke
• ./scripts/reproduce_paper.sh --smoke --include-llm-benchmark