4-hour Notre Dame faculty seminar on agentic AI for academic research — Quarto slides + curated demo bundle. Companion to claude-code-my-workflow.
Skill Claude CodeCodex
Enforce the replication-protocol.md rule by cross-checking numeric claims in a manuscript against the actual R / Stata / Python outputs. Report PASS/FAIL per claim against tolerance thresholds. Use before submission and before releasing a replication package.
Skill Claude CodeCodex
Save a structured state snapshot before stopping or handing off. Captures the active plan, recent decisions, file pointers (with line numbers), open questions, and the next 1–3 actions into a checkpoint file under qualityreports/checkpoints/. Optionally proposes [LEARN] entries to add to MEMORY.md. Use when user says…
Skill Claude CodeCodex
Stage, commit, push, open a PR, and merge to main. Use ONLY on explicit commit intent — user says "commit", "ship it", "push this", "open a PR", "merge to main", "let's commit this", or prefixes with /commit. Do NOT auto-invoke on vague end-of-task phrases ("we're done", "wrap up") — those require explicit…
Skill Claude CodeCodex
Deep consistency audit of the entire repository infrastructure. Launches 4 parallel specialist agents to find factual errors, code bugs, count mismatches, and cross-document inconsistencies. Then fixes all issues and loops until clean. Use when: after making broad changes, before releases, or when user says "audit"…
Skill Claude CodeCodex
Adversarial 5-7 question challenge to a deck's pedagogical choices — ordering, prerequisites, cognitive load, motivation. Use when user says "devil's advocate", "poke holes in this deck", "push back on my slides", "stress-test the design", "what would a skeptical student ask?". Read-only; surfaces questions to force…
Skill Claude CodeCodex
Structured literature search + synthesis with citation extraction, thematic clustering, and gap identification. Use when user says "find papers on X", "do a lit review", "what's the literature on...", "summarize what we know about...", "where's the gap in this field", "review recent work on Y". Produces a written…
Skill Claude CodeCodex
Convert a PDF (or any document) to clean markdown so Claude can read it efficiently. Tries Microsoft MarkItDown first; falls back to OpenDataLoader-PDF for complex layouts (multi-column papers, dense tables, math). Use when user says "convert this PDF", "make this document readable", "turn paper.pdf into markdown"…
Skill Claude CodeCodex
Run holistic pedagogical review on lecture slides. Checks narrative arc, PhD student prerequisites, worked examples, notation clarity, and deck pacing.
Skill Claude CodeCodex
Draft a structured preregistration document (OSF, AsPredicted, or AEA RCT Registry style) from a research spec or free-form study description. Output is a Markdown file with hypotheses, design, sampling plan, analysis plan, exclusions, and inference criteria — annotated with MUST / SHOULD / MAY clarity flags. Use when…
Skill Claude CodeCodex
Read-only proofreading pass over lecture .tex or .qmd files. Checks grammar, typos, overflow, terminology consistency, and academic writing quality; produces a report without editing. Use when user says "proofread", "check for typos", "look for grammar issues", "copy-edit this", "any writing errors?", or before a…
Skill Claude CodeCodex
Adversarial QA workflow comparing Quarto HTML against Beamer PDF benchmark. Iterates between critic (finds issues) and fixer (applies fixes) until APPROVED or max iterations reached.
Skill Claude CodeCodex
Generate a structured response-to-referees document from a referee report and the revised manuscript. Maps each referee comment to the specific revision, classifies coverage (addressed / partially / deferred / disagreement), and drafts polite but firm responses. Use during the R&R (revise-and-resubmit) stage of paper…
Skill Claude CodeCodex
Comprehensive manuscript review with three modes: single-pass (default), --adversarial critic-fixer loop, and --peer [journal] simulated peer-review pipeline (editor + 2 dispositioned referees + editorial decision, calibrated to a target journal). R&R continuation via --peer --r2/--r3; hostile-editor stress test via…
Skill Claude CodeCodex
Comprehensive slide excellence review combining visual audit, pedagogical review, and proofreading. Produces three reports and a combined summary.
Skill Claude CodeCodex
Validate bibliography entries against citations in all lecture files. Structural checks (missing/unused entries, malformed fields) by default; --semantic adds citation-drift detection, DOI verification, and style-consistency checks.
Skill Claude CodeCodex
Run Chain-of-Verification (CoVe) on a draft or a block of text with factual claims. Spawns the claim-verifier agent in a forked (fresh) context so it never sees the draft — then reports which claims are supported, contradicted, or unverifiable. Use when user says "verify these citations", "check the claims in X", "did…
Skill Claude CodeCodex
Perform adversarial visual audit of Quarto or Beamer slides checking for overflow, font consistency, box fatigue, and layout issues.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: