claude-code-my-workflow

In the author's own words, from each skill's SKILL.md — showing the first 30 of 61 files.

• adjudicate-review

  Turn an incoming set of findings — from an AI reviewer, a referee report, a code review, a linter, or a second model — into verified fixes, without letting a confident misread damage correct work. Every finding is a CANDIDATE until checked against the actual source. Use whenever you receive review comments, audit findings, or a critique you did not write yourself, especially when the reviewer is…

  .claude/skills/adjudicate-review/SKILL.md on GitHub (opens in a new tab)

• audit-reproducibility

  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.

  .claude/skills/audit-reproducibility/SKILL.md on GitHub (opens in a new tab)

• blast-radius

  Before and after changing anything shared — a function's return value, a signature, a schema, a label set, a config default, a constant, a file format — find every consumer and actually run them. Catches the change that looks purely additive but silently breaks a contract in a file you never opened. Use when editing shared code, adding a field/column/return element, renaming, changing units or de…

  .claude/skills/blast-radius/SKILL.md on GitHub (opens in a new tab)

• capture-environment

  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 use…

  .claude/skills/capture-environment/SKILL.md on GitHub (opens in a new tab)

• challenge

  Stress-test a finding against the choices you did not make. Enumerates the discrete forks a competent analyst could have taken (measure definition, sample filter, control set, clustering level, weighting, functional form), runs the specification grid, and reports the distribution rather than a point estimate — then attacks the identifying assumption with named, computable sensitivity statistics.…

  .claude/skills/challenge/SKILL.md on GitHub (opens in a new tab)

• checkpoint

  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 u…

  .claude/skills/checkpoint/SKILL.md on GitHub (opens in a new tab)

• coauthor-brief

  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 change…

  .claude/skills/coauthor-brief/SKILL.md on GitHub (opens in a new tab)

• commit

  Commit the current work — runs the quality, consistency and passport gates, branches off main if needed, stages specific files, and writes a commit whose subject states what is now true. Pushes and opens a pull request only with --pr or when the user asks; never merges — a merge happens only when the user explicitly says to merge. Use ONLY on explicit commit intent — user says "commit", "let's co…

  .claude/skills/commit/SKILL.md on GitHub (opens in a new tab)

• compile-latex

  Compile a Beamer LaTeX slide deck with XeLaTeX (3 passes + bibtex). Use when user says "compile", "build the slides", "rebuild the PDF", "run latex", "render the tex", or asks why a `.tex` file isn't producing a PDF. Operates on `Slides/*.tex`.

  .claude/skills/compile-latex/SKILL.md on GitHub (opens in a new tab)

• compress-session

  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…

  .claude/skills/compress-session/SKILL.md on GitHub (opens in a new tab)

• context-status

  Show current context status and session health. Use to check how much context has been used, whether auto-compact is approaching, and what state will be preserved.

  .claude/skills/context-status/SKILL.md on GitHub (opens in a new tab)

• create-lecture

  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`).

  .claude/skills/create-lecture/SKILL.md on GitHub (opens in a new tab)

• credible-claims

  Research-brief + claim-record discipline for delegated or AI-assisted research work. Use when starting any substantive research task or long autonomous run (write the brief first), and when reporting results that will support a claim in a paper or decision (produce the claim record). Keeps faster execution from being confused with credible evidence.

  .claude/skills/credible-claims/SKILL.md on GitHub (opens in a new tab)

• data-analysis

  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 `ou…

  .claude/skills/data-analysis/SKILL.md on GitHub (opens in a new tab)

• data-management-plan

  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 g…

  .claude/skills/data-management-plan/SKILL.md on GitHub (opens in a new tab)

• deep-audit

  Comprehensive adversarial audit of a theory, proof, math/econ paper, codebase, or set of claims — decompose into components, fan out independent skeptics that must return CONCRETE defects, adjudicate every finding with a separate judge, fix all confirmed defects, then re-verify. Use when correctness must be bulletproof and single-pass or round-by-round review is too slow and too shallow. Invoke f…

  .claude/skills/deep-audit/SKILL.md on GitHub (opens in a new tab)

• deploy

  Render Quarto `.qmd` slides to HTML and sync to `docs/` for GitHub Pages. Use when user says "deploy", "publish the slides", "ship to pages", "push the lecture live", "render and publish", or after Quarto edits that need to go public. NOT for local Quarto render only — use `quarto render` directly for that.

  .claude/skills/deploy/SKILL.md on GitHub (opens in a new tab)

• devils-advocate

  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 rethinking. Lighter than `/pedagogy-review`.

  .claude/skills/devils-advocate/SKILL.md on GitHub (opens in a new tab)

• diagnose

  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):…

  .claude/skills/diagnose/SKILL.md on GitHub (opens in a new tab)

• differential-audit

  Compare two implementations of the same thing — a port (R↔Python↔Stata), a reimplementation, a replication package, a refactor, or a new version against the old — so that agreement means something. Freeze inputs first, inventory every expected output, test the comparator itself, compare every channel (not just the headline number), and give each divergence a stable ID and a smallest witness. Use…

  .claude/skills/differential-audit/SKILL.md on GitHub (opens in a new tab)

• disclosure-check

  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 CRI…

  .claude/skills/disclosure-check/SKILL.md on GitHub (opens in a new tab)

• extract-tikz

  Extract TikZ diagrams from Beamer `.tex` source, compile each to a standalone PDF, and convert to SVG with 0-based indexing. Use when user says "extract the tikz", "regenerate the diagrams", "rebuild the SVGs", "sync tikz to quarto", or after editing TikZ blocks in a Beamer deck that also has a Quarto mirror.

  .claude/skills/extract-tikz/SKILL.md on GitHub (opens in a new tab)

• grant-proposal

  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…

  .claude/skills/grant-proposal/SKILL.md on GitHub (opens in a new tab)

• humanize

  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; d…

  .claude/skills/humanize/SKILL.md on GitHub (opens in a new tab)

• interview-me

  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 f…

  .claude/skills/interview-me/SKILL.md on GitHub (opens in a new tab)

• issues

  Keeps a project's to-do list and memory in GitHub issues — files each finding (from a review, an audit, or the user) as its own issue without duplicates, lists the open issues that bear on the current work, and closes an issue with a comment recording what was wrong, what was tried, what worked, and how it was fixed. Use when review findings or a list of problems should become tracked work (a pap…

  .claude/skills/issues/SKILL.md on GitHub (opens in a new tab)

• learn

  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.

  .claude/skills/learn/SKILL.md on GitHub (opens in a new tab)

• lit-review

  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.

  .claude/skills/lit-review/SKILL.md on GitHub (opens in a new tab)

• new-diagram

  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.

  .claude/skills/new-diagram/SKILL.md on GitHub (opens in a new tab)

• new-skill

  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…

  .claude/skills/new-skill/SKILL.md on GitHub (opens in a new tab)

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