claude-academic-setup: Instructions file for Codex

AGENTS.md

Precedence: system/developer constraints > explicit user request > project AGENTS.md > this file. If a named skill or tool is unavailable, use the closest available workflow.

1. Use Skills When Relevant

When starting a new task, check for clearly relevant skills and use them first. Key triggers:

• Session start -> napkin
• New data -> datacheck
• Plots -> viz
• Prose -> plain-writing. Default for docs and general-audience prose. For expert or academic writing, keep field terms and stay concise.
• Creative work -> brainstorming

Use request_user_input for structured questions when that tool is available. Fall back to concise plain-text questions otherwise.

2. Think Before Coding

• State assumptions.
• If uncertain, ask.
• Multiple interpretations -> present them, don't pick silently.
• If a simpler approach exists, say so.

3. Simplicity First

• No features, abstractions, or error handling beyond what's needed.
• Prefer concise solutions. If it looks overcomplicated, simplify.

4. Surgical Changes

• Don't improve, refactor, or reformat code you weren't asked to change.
• Match existing style. Assume the worktree may be dirty.
• Remove only orphans created by your own changes.
• Exception: visual/UI tasks should present cohesive updates, not fragmented line edits.

5. Reproducible Evidence

When running substantive analysis, not one-liners or sanity checks:

• Capture output via tee to logs/YYYY-MM-DD_HH-MM-SS_<description>.log.
• Keep logs/ in .gitignore. Never commit logs.
• Never report results without evidence the code actually ran, such as a log, notebook output, or test report.

6. Git

• Inspect status and diffs before changing or committing files.
• Do not discard work you did not create.
• Never include Co-Authored-By in commit messages.

7. Prose & Markdown Line Breaks

• Never hard-wrap prose. Write each paragraph as one continuous line and let the editor soft-wrap.
• Insert newlines only between block elements (paragraphs, list items, headings, table rows, code blocks) — never mid-sentence or at a fixed column width.
• Applies to all .md, .txt, and general prose output. Exceptions: git commit message bodies (wrap at ~72), and files whose existing content is already hard-wrapped (match the file).
• When editing an existing prose file that is hard-wrapped and the user asks for content changes, don't silently reflow it; ask first.