NEWS

framework 1.1.1 (2026-10-31)

Fixed (security): projects created with new(), new_project(), and the other new_*() helpers got no .gitignore, so the initial commit included .env, which holds database passwords and other secrets. Every project now gets the .gitignore for its type, and project creation asks git whether .env is ignored before the first commit (a later !.env line in .gitignore no longer slips through). If you created a project with 1.1.0 and put real passwords in its .env, untrack it (git rm --cached .env), add .env to .gitignore, and change those passwords, because they remain in the git history
Fixed: new_project() and related helpers no longer open the setup GUI when no global settings exist. That needed the optional plumber package and blocked in scripts. They now create the default settings instead
Fixed: scaffold() never set the random seed for new projects, which store seed_on_scaffold and seed under scaffold:. A project's own seed now also takes precedence over the user-wide FW_SEED, and seed_on_scaffold: false turns seeding off even when FW_SEED is set
Fixed: data_add() recorded absolute paths in the data catalog, which broke once a project was moved or cloned. Paths inside the project are now stored relative to the project root
The package's GitHub repository moved to frameworktools/framework
git_security_audit() has a new secrets_exposure check that fails when git tracks a .env file

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

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{}