claude-code-my-workflow

Generate the submission-time disclosure block for a manuscript — the AI-use disclosure statement matched to the target journal's policy, CRediT author-contribution roles, conflict-of-interest statement, and data-availability statement. Use when the user says "AI disclosure", "disclosure statement", "do I need to disclose Claude", "CRediT roles", "conflict of interest statement", "data availability statement", or is preparing a submission package. NOT statistical-disclosure screening of restricted-data outputs — that is /disclosure-check.

Root-cause a failing or wrong empirical result with a disciplined reproduce → minimise → hypothesise → instrument → fix loop, instead of guessing-and-poking. Use when the user says "why is my regression wrong", "this number changed", "my script errors out", "the result won't reproduce", "debug this", "this estimate looks wrong", or "it worked yesterday". Tuned for research code (R/Stata/Python): type coercion, NA/merge blow-ups, factor levels, clustering/SE choices, weighting, collinearity/convergence, seeds, package-version drift. Use `--no-fix` to localize the root cause without editing shared or load-bearing files.

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.

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", "find inconsistencies", "check everything".

Create a new Beamer lecture `.tex` from source papers and materials, with notation consistency checks and the project's preamble wired in. Use when user says "create a lecture on X", "new lecture from these papers", "start a deck on topic Y", "scaffold a new Beamer file", "build me a lecture from these PDFs". Scaffolds the full deck — NOT for compiling existing `.tex` (use `/compile-latex`).

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 --peer --stress; reviewer-disposition variance reporting via --peer --variance N. Auto-invokes /review-r + /audit-reproducibility on referenced scripts unless --no-cross-artifact.

Run a staggered difference-in-differences / event-study analysis to the Sant'Anna practitioner standard — drives the canonical packages (R `did`/`DRDID`/`didFF`/`contdid`; Stata `csdid`/`drdid`), enforces the doubly-robust default, a mandatory diagnostic + sensitivity suite, uniform-band inference, replicate-and-verify-against-source discipline, and ends in a graded credibility verdict. Use when user says "run a DiD", "event study", "staggered adoption", "Callaway Sant'Anna", "att_gt", "csdid", "did with multiple periods", or points at panel data with a treatment-timing variable. NEVER reimplements an estimator.

Compute statistical power, required sample size, and minimum detectable effect (MDE) for a study design, then write a registry-ready power section. Handles two-arm RCTs (with clustering / ICC and unequal allocation), multiple-arm corrections, and a simulation-based power option for non-standard designs (DiD/event-study, IV, panel). Use when user says "power analysis", "power calculation", "MDE", "minimum detectable effect", "how big a sample do I need", "is my study powered", "power for an RCT", or when /preregister needs a power section for an experiment. Produces a power/MDE table, power curves, and a methods paragraph to paste into a preregistration.

Scaffold a new skill that follows this repo's conventions — interviews for purpose, trigger phrases, and tool needs, then writes `.claude/skills/<name>/SKILL.md` from the skill template with frontmatter and body that pass the integrity gates on first try. Use when user says "write a skill", "scaffold a skill", "create a new skill", "I keep doing X, make it a skill", "new slash command", or "turn this workflow into a skill". NOT for capturing a one-off session discovery — that is `/learn`.

Turn student course evaluations (free-text + numeric) into an actionable teaching-improvement plan — the teaching analogue of /respond-to-referees. Clusters comments into themes, separates signal from noise, classifies each theme Keep / Change / Investigate / Out-of-scope, and drafts concrete changes mapped to the syllabus and slide decks. Use when user says "respond to my evals", "what do these course evaluations tell me", "turn my teaching feedback into a plan", or after a semester's evals arrive.

Scaffold a graded problem set with sections, problems, worked solutions, and short "why this matters" explainers across analytical, empirical, and coding types. Use when user says "make a problem set on X", "scaffold exercises for this lecture", "create practice problems", "generate homework with a solution key", "build a graded assignment on topic Y". Emits a clean student set plus a separate solution key — NOT for grading submissions or auto-checking student answers.

Build or restructure a course syllabus from a topic list or reading list — course description + prerequisites, week-by-week schedule (topic → readings → deliverables), measurable learning objectives, an assessment scheme + rubric, standard policies (late work, AI use, academic integrity, accessibility), and a per-week work-list to hand to `/create-lecture`. Use when user says "build a syllabus", "structure my course", "turn this reading list into a schedule", "draft a course outline", "make a syllabus for Econ 7xx", or "map weeks to lectures". Economics-aware (PhD metrics/micro/macro sequences, undergrad); generic enough for any field.

Turn a research paper into teaching materials — a lecture outline, the 3-5 results worth presenting (with intuition), a slide skeleton ready for `/create-lecture`, discussion questions, and a problem-set brief. Reads the paper end-to-end and pitches to a stated audience level. Use when user says "turn this paper into a lecture", "teach from this paper", "build slides from this PDF", "make teaching materials from X", "I'm presenting this paper to my class".

Triage academic email and calendar (Gmail / Google Calendar via the session's MCP) into a prioritized digest plus a referee-obligations tracker — classifying referee requests, R&R and editor correspondence, co-author threads, seminar and conference invites, and grant/admin deadlines, and proposing a human-gated action for each (draft reply, calendar hold, scaffold a project, snooze). Use when user says "triage my inbox", "check my academic email", "what needs my attention this week", "go through my mail", or when run as a scheduled routine. NEVER auto-sends or auto-accepts anything.

Snapshot the computational environment for a replication package — detects the analysis stack (R / Stata / Python) and emits the right lockfiles (renv.lock + sessionInfo.txt, requirements.txt / environment.yml / uv.lock, Stata version + ado package list), records seeds and RNG kind, optionally writes a pinning Dockerfile, and produces a paste-ready "Computational requirements" block. Use when user says "capture the environment", "snapshot my dependencies", "pin the versions", "make a renv.lock / requirements.txt", "make this byte-reproducible", or before releasing a replication package to openICPSR / the AEA Data Editor.

Generate a co-author / collaborator handoff brief for a multi-author, multi-machine project — summarizing what changed since the last brief (git delta), the current state of each artifact (manuscript, analysis, slides), open questions, how to reproduce locally, and any restricted-data access steps. Use when user says "coauthor brief", "handoff brief", "bring my coauthor up to speed", "what changed since last week", "onboard a collaborator", "write a handoff for [name]", or before sending a co-author the repo. NOT a commit or a checkpoint — it is the cross-machine, cross-person summary `meta-governance.md` only partially covers.

Draft a funder-compliant Data Management Plan (NSF DMP, NIH DMS Policy 2023, ERC, Horizon Europe) by composing the confidential-data and environment-capture primitives. Sections cover data description, formats/metadata, storage/backup, access/sharing, preservation/archiving, and roles. Use when user says "data management plan", "DMP", "DMSP", "NIH data sharing plan", "write the data plan for my grant", or when a grant proposal needs a data-management section. NOT a submission tool — produces a draft the user pastes into the funder portal (DMPTool, NIH ASSIST, Horizon Europe portal).

Pre-screen analysis outputs (tables, figures, logs) built on restricted or confidential data for statistical-disclosure-limitation problems before any release. Scans for small cell counts, complementary-suppression gaps, dominance (p-percent / (n,k)), re-identifiable exact counts, PII leakage, and unrounded sensitive statistics; classifies each finding CRITICAL / WARNING / OK and gates on any CRITICAL. Use before depositing or sharing restricted-data results, or when the user says "disclosure check", "SDL scan", "is this output safe to release", "check for small cells", "disclosure avoidance", "pre-screen for the RDC", or "can I export this from the enclave".

Scaffold a research grant proposal (NSF, NIH, ERC, or foundation) by composing existing primitives — pulls identification strategy from an `/interview-me` spec, delegates the data-management plan to `/data-management-plan` and the facilities statement to `/capture-environment`, and emits a funder-requirements checklist. Use when user says "draft a grant", "write a proposal", "NSF proposal", "NIH aims", "ERC application", "foundation grant", "specific aims", or "scaffold a grant proposal". NOT a submission tool — produces a draft the user uploads to the sponsor's portal themselves.

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 user says "preregister", "draft a preregistration", "OSF preregistration", "AsPredicted", "AEA RCT registry", "PAP", "preanalysis plan", or before launching an experiment / data collection / analysis on data the analyst has not yet seen. NOT a registry submission tool — produces a document the user uploads to OSF / AsPredicted / AEA themselves.

Assemble a submission-ready replication package to the AEA Data and Code Availability Standard (DCAS) / openICPSR / Social Science Reproduction Platform expectations — standard replication README, dataset manifest, computational-requirements capture, a Table/Figure → script:line map, and a confidential-data deposit plan. Use when user says "build the replication package", "prepare the openICPSR deposit", "make the AEA data and code package", "DCAS compliance", "assemble the deposit for the journal", or after a paper is accepted and the journal's data editor needs the package. NOT a numeric verifier — it calls /audit-reproducibility to confirm claims reproduce before packaging.

Adversarial Quarto-vs-Beamer parity QA. A critic agent compares the Quarto HTML render to the Beamer PDF benchmark for content/visual parity; a fixer agent applies fixes; loops until APPROVED (max 5 rounds). Use when user says "qa the quarto", "check parity", "does the html match the pdf?", "quarto matches beamer?", or after a translate-to-quarto run. Requires both the `.qmd` rendered and a `.pdf` benchmark.

Mechanize Pattern 15 — the seven-pass adversarial review protocol for academic manuscripts. Spawns 7 forked subagents in parallel (abstract, intro, methods, results, robustness, prose, citations), then synthesizes a prioritized revision checklist. Use for submission-ready or R&R-stage papers where single-pass review isn't enough.

Multi-agent comprehensive slide review (visual + pedagogy + proofreading, plus TikZ / parity / substance conditionally). Use when user says "full review", "excellence pass", "comprehensive check", "review everything", "pre-release review", "slide excellence", or before teaching / shipping a deck. Fanout wrapper — for a single lens, use `/visual-audit`, `/pedagogy-review`, or `/proofread` directly.

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.

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 I hallucinate anything", "fact-check this draft", "run CoVe on this", or after any text generation that asserts facts about papers, datasets, or numerical results. NOT for style/grammar review (use `/proofread`) or substance review (use `/review-paper`).

Review candidate `[LEARN]` entries in `.claude/state/personal-memory.md` (gitignored) and run them through a five-critic council in parallel: generality, staleness, redundancy, evidence, format. Majority vote (3+ of 5) promotes the entry to MEMORY.md. Use when user says "promote memory", "review my learnings", "what should graduate to MEMORY.md", "five-critic council", or as monthly memory maintenance.

Run the full R package release gate — regenerate docs, run the test suite, run R CMD check --as-cran, and triage every ERROR / WARNING / NOTE against CRAN policy before a release or submission. Use when the user says "check my R package", "R CMD check", "is this package CRAN-ready", "run devtools::check", "prepare for CRAN submission", or points at a directory containing a DESCRIPTION file. Produces a check report + CRAN-submission checklist in `quality_reports/`.

Scaffold and run a reproducible Monte Carlo simulation study in R — parameterized DGP, an estimator grid, a seeded replication loop, and a summary of bias, RMSE, empirical SE, coverage, size/power with Monte Carlo standard errors. Use when the user says "run a Monte Carlo simulation", "simulation study", "check the bias/coverage of an estimator", "compare estimators in simulation", "size and power simulation", "Monte Carlo experiment", or wants to demonstrate an estimator's finite-sample properties. Produces a numbered R script in `scripts/R/` and saves per-replication raw results + a summary table to `scripts/R/_outputs/`.

End-to-end Stata replication pipeline — scaffolds numbered `.do` files in `scripts/stata/`, executes them via the `stata-mcp` MCP server, captures logs and outputs to `scripts/stata/_outputs/`, and produces publication-ready tables (esttab) and figures (graph export). Mirrors `/data-analysis` for R-first projects. Use when user says "stata replication", "set up Stata pipeline", "scaffold the .do files", "run Stata analysis", "AEA replication package in Stata", or when a project's analysis language is Stata not R.

Distill the current conversation into a structured note (decisions made, open questions, file pointers with line numbers, next 1–3 actions) and save to `quality_reports/session_logs/` before auto-compression. Differs from `/checkpoint` (explicit stop-point snapshot) and from auto-compaction (which truncates rather than distills). Use when context is approaching auto-compact threshold, when a long pipeline has accumulated many decisions, or when the user says "compress", "distil this session", "before we hit auto-compact", "structured handoff before context resets".

Read-only audit of `.tex`, `.qmd`, or `.md` text for AI-voice tells — boilerplate transitions ("Moreover", "Furthermore", "It is important to note that"), AI-cliché lexicon ("delve", "navigate the complexities", "tapestry", "robust framework"), em-dash overuse, symmetric paragraph shapes, tricolon abuse, hedging stacking, "not only X but also Y" frames, and formulaic openers. Produces a report; does NOT rewrite. Use when user says "humanize", "does this sound like AI?", "check for AI tells", "de-AI this draft", "remove AI voice", "audit my prose for sycophancy", or before journal submission / posting a working paper.

Interactive interview that formalizes a fuzzy research idea into a structured spec (RQ, hypotheses, identification, data needs, empirical strategy). Use when user says "interview me", "help me think through this idea", "I have a half-baked idea", "formalize this into a project", "walk me through framing a study". Multi-turn Q&A; saves spec to disk. NOT for lit review (`/lit-review`) or ideation from scratch (`/research-ideation`).

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 `quality_reports/checkpoints/`. Optionally proposes `[LEARN]` entries to add to MEMORY.md. Use when user says "checkpoint", "save state", "snapshot before I stop", "where am I", "wrap up the session for handoff", or before a long break / model switch / collaborator handoff. Companion to (NOT replacement for) the narrative session-log workflow.

End-to-end R data analysis pipeline — exploration → cleaning → regression → publication-ready tables and figures. Use when user says "analyze this dataset", "run a regression on X", "explore this CSV", "full analysis workflow", "get me summary stats and a regression", or points at a `.csv`/`.rds`/`.dta` and asks for empirical results. Produces numbered R scripts in `scripts/R/` and outputs to `scripts/R/_outputs/`.

Extract reusable knowledge from the current session into a persistent skill. Use when you discover something non-obvious, create a workaround, or develop a multi-step workflow that future sessions would benefit from.

Scaffold a new TikZ diagram from the snippet gallery with prevention rules pre-applied (explicit node dimensions, coordinate map, directional edge labels). Compiles standalone, invokes tikz-reviewer with citations from tikz-measurement.md, and loops on revisions until APPROVED.

Generate structured research questions, testable hypotheses, and candidate empirical strategies from a topic, phenomenon, or dataset description. Use when user says "give me research ideas on X", "brainstorm questions about Y", "what could I study with this data?", "I'm looking for a paper idea on...", "generate hypotheses for...". One-shot generation, not multi-turn. For idea-refinement use `/interview-me`.

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 review with BibTeX-ready citations. Uses WebSearch/WebFetch for recent work.

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 revision.