framework 1.1.0

plumber moved from Imports to Suggests. plumber pulls in sodium, which needs the system libsodium library and often fails to install on HPC clusters. The GUI (gui(), setup()) now asks you to install plumber when you launch it; nothing else needs it
New standard logs directory for run logs and cluster job output. All project gitignore templates now ignore **/logs/** and slurm-*.out, and security_audit() treats logs as a private directory
scaffold() git checks are now portable across platforms
Skills-based AI context: new projects get a thin canonical AGENTS.md plus Framework skills installed in .claude/skills/ (workflow, data, packages, outputs, and sensitive-data rules as separate SKILL.md files)
AGENTS.md replaces CLAUDE.md as the default canonical AI context file; CLAUDE.md and .github/copilot-instructions.md are now thin pointer stubs
New ai_skills_update() refreshes a project’s Framework skills after upgrading the package
ai_regenerate_context() falls back to CLAUDE.md for projects created before 1.1.0

framework 1.0.0

Fixed non-ASCII characters in R source files for CRAN compatibility
Fixed documentation for subdir parameter in make_rmd(), make_revealjs(), and make_presentation()
Added missing package declarations to DESCRIPTION Suggests
Improved scratch_capture() examples with \dontrun{}