Add Copilot setup workflow for R package development

[Copilot]

This PR adds a .github/workflows/copilot-setup-steps.yml workflow to onboard the TreeTools repository for GitHub Copilot coding agent support.

What this enables

The workflow provides a complete development environment setup for Copilot agents working on TreeTools, including:

• R environment: Latest R release with all TreeTools dependencies
• System dependencies: LaTeX (texlive) for documentation, C++17 compiler for native code
• Development tools: devtools, testthat, roxygen2, lintr, rcmdcheck
• Package-specific setup: phangorn dependency with version constraints, CRAN-like environment variables

Technical details

The workflow is based on the existing R-CMD-check.yml but simplified for single-platform agent use:

• Uses ubuntu-latest instead of matrix builds
• Includes needs: check, coverage for comprehensive dependency resolution
• Sets minimal permissions (contents: read)
• Follows GitHub's copilot-setup-steps template requirements

Agent capabilities enabled

With this setup, Copilot agents can:

• Build and check R packages (R CMD build, R CMD check)
• Run the full test suite with testthat
• Perform code linting with the existing .lintr configuration
• Generate documentation with roxygen2
• Install and manage dependencies automatically

The workflow triggers on manual dispatch and when the setup file is modified, allowing for easy validation and testing.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• r-lib.github.io
  • Triggering command: /usr/lib/R/bin/exec/R -s -e curl::curl_download("REDACTED","get-libgit2-linux.sh") (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

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✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.