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Publication repository guidance

Human authorship boundary

Publications created from this template and any related blog posts must remain human-authored. Agents may operate the publishing machinery, but they must not supply the writing, analysis, or scientific reasoning.

  • Do not draft, rewrite, paraphrase, polish, translate, or autocomplete publication or blog prose. This includes titles, summaries, body text, captions, appendices, disclosures, contribution statements, and repository prose such as README or CONTRIBUTING text.
  • Do not invent or add scientific claims, methods, results, interpretations, citations, examples, mathematical arguments, or analysis code whose output supports a scientific conclusion.
  • Do not directly apply grammar, style, clarity, citation, or mathematical corrections to authored content. A human author must decide and make the final change.
  • Text or analysis code supplied by a human may be inserted verbatim when the user explicitly directs where it belongs. Do not silently revise it while inserting it.
  • Do not author AI-use disclosures or CRediT statements on anyone else's behalf. Agents may validate author-supplied records and report omissions.

Agents may:

  • Compile, render, convert, package, and debug Quarto, Jupyter, LaTeX, HTML, and PDF outputs.
  • Work on CI, configuration, templates, stylesheets, layout, accessibility, and web design without changing authored prose, analyses, or scientific meaning.
  • Run human-authored analysis code to reproduce outputs and report failures without changing the analysis.
  • Inspect human-authored writing and return a checklist of possible grammar problems, awkward sentences, unclear passages, citation problems, or mathematical inconsistencies. Give that checklist in chat or an untracked local review artifact; never commit or push it, and never apply its proposed edits automatically.

Before every commit or push, inspect the complete diff. If it contains agent-authored publication or blog prose, scientific analysis, or scientific reasoning, remove that content from the change and stop for a human author to provide it. Do not transfer AI-written prose between this template, a derived publication repository, or a blog repository. This AGENTS.md policy is an explicitly authorized exception.

Repository safety

  • Do not commit generated _site/, .quarto/, rendered notebook support directories, local caches, or environment directories.
  • Do not commit session notes, design drafts, implementation plans, private correspondence, credentials, or other agent-specific artifacts.
  • Preserve author-approved metadata and disabled-by-default tracking and comment settings.
  • Work on a focused branch and submit changes through a pull request.

Verification

Before requesting review, run the relevant tests and render both publication profiles:

make test
make render-warm
make render-technical

Review the rendered pages for layout, links, citations, metadata, and disclosure placement without editing the authored content.