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AGENTS.md

Repository guidance for human and AI contributors.

Scope

Use this file as the local operating guide when modifying kaefa.

Key Paths

Core orchestration: R/kaefa.R
Estimation engine: R/newEngine.R
Shared helpers: R/utils.R
Shiny app: inst/shiny-app/app.R
Tests: tests/testthat/
CI and security gates: .github/workflows/

Working Rules

Keep external behavior stable unless an issue/PR explicitly changes it.
Prefer minimal, targeted edits over broad refactors.
If docs are generated (README.Rmd -> README.md), regenerate in the same commit when source docs change.
Never commit secrets (.env, keys, tokens, credentials).

Verification Checklist

For every change, run what is relevant to the touched files:

Markdown docs: npx -y markdownlint-cli2@0.20.0 <files...> (requires Node.js and npm)
R package checks: required GitHub checks on PR (R-CMD-check, dependency-review)
Targeted local validation for touched package behavior when applicable

Optional R Code Validation

Style lint (optional): run lintr on changed R files.
Shiny smoke run (optional): launch launchAEFA() for UI-touching changes.
Tests (optional): run devtools::test() or targeted testthat files.

Review and Merge

Resolve all review threads.
Ensure required checks are green.
Obtain approval before merge.