flonat
UserShareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows
Categories
Indexed Skills (50)
beamer-deck
Create an academic presentation as a LaTeX Beamer source and reviewed PDF with an original theme. Use when the requested deliverable is a conference, seminar, or lecture deck in Beamer. Not for PowerPoint or RevealJS; use $pptx or $quarto-deck.
bib-parse
Extract citations from a PDF and generate a validated .bib file. Use when the user asks to extract citations from a PDF and generate a validated .bib file. Reads the PDF, identifies referenced works, constructs BibTeX entries, and verifies metadata.
causal-design
Design or audit the identification strategy for an observational study. Use when the task concerns estimands, causal assumptions, threats to identification, or defensible research design rather than model implementation.
computational-experiments
Scaffold, execute, analyse, and publish computational research experiments through a reproducible staged workflow. Use when a research question requires simulations or computational sweeps rather than a one-off script.
data-analysis
Deliver an end-to-end analysis pipeline: EDA, estimation, or publication output. Use when the user requests an end-to-end analysis pipeline: EDA, estimation, or publication output.
interview-me
Conduct an adaptive structured interview that elicits tacit knowledge, requirements, preferences, or decisions and summarizes them explicitly. Use when the needed information is in the user's head and cannot be recovered from project files. Not for adversarial oral examination; use $grill-me.
knowledge-lint
Lint an existing project knowledge base for contradictions, uncited claims, missing connections, stale articles, and orphaned concepts. Use when checking the integrity of already compiled knowledge before relying on or expanding it. Not for compiling raw sources; use $compile-knowledge.
latex-polish
Inspect a cleanly compiling LaTeX document for source pathologies and rendered visual defects by linting and viewing selected PDF pages. Use when compilation succeeds but title pages, floats, tables, figures, or layout still need publication-quality review. Not for basic compilation health; use $latex-health-check.
latex-scaffold
Convert an existing Markdown manuscript draft into a buildable LaTeX project with canonical structure and build configuration. Use when prose already exists but no LaTeX source tree does. Not for checking template drift in an existing project; use $latex-template.
latex-template
Compare a project's LaTeX preamble and conventions against the canonical working-paper template. Use when diagnosing template drift without converting venue formats or editing prose.
latex
Compile one specified LaTeX document, resolve build errors, audit citations, and report build quality. Use when a .tex source must be built or a concrete compilation failure repaired. Not for corpus-wide build checks, visual polish after a clean build, or creating a project; use $latex-health-check, $latex-polish, or $latex-scaffold.
method-audit
Extract and compare data-collection methods across a set of empirical papers. Use when the user needs a cross-paper methods matrix or wants to assess how a literature gathers evidence.
multi-perspective
Explore a research question through several independent analytical perspectives and synthesize their agreements and disagreements. Use when one line of reasoning is insufficient and distinct viewpoints should be preserved.
pre-submission-report
Run the final, comprehensive submission-readiness gate and consolidate all checks into one dated report; citation-integrity-only mode is also supported. Use when a paper and submission package are nearly final. Not for a mid-draft adversarial review; use $review-cluster.
proofread
Proofread a LaTeX academic paper across eleven language, notation, citation, and consistency categories. Use when the requested task is bounded proofreading rather than substantive rewriting, clarity stress-testing, or venue compliance.
bib-coverage
Compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries. Use when the user asks to compare a project .bib against a Paperpile project/topic folder to find uncited papers or unfiled entries.
bib-filter
Filter a LaTeX project's bibliography to the entries actually cited, with Overleaf-source resolution, temporary staging, validation, approval-gated canonical replacement, and compilation. Use before submission or after large revisions.
brief-compliance-check
Check a LaTeX coursework submission against the requirements in a supplied PDF assessment brief. Use when verifying format, required sections, word limits, or deliverables before submission. Not for general prose proofreading; use $proofread.
camera-ready
Convert an accepted anonymous-submission LaTeX paper (AAAI/AIES/ACM-style) to camera-ready and implement the accepted reviews. Use when a paper is accepted with no rebuttal and you need to de-anonymize, add copyright, turn on section numbering, implement each reviewer's minor revisions, optionally move proofs to a non-counted appendix, and QA. Not for R&R/revise-and-resubmit (use strategic-revision --external) or for preprints (use preprint).
checkpoint
Save a compact continuation checkpoint so current work survives context compaction or a later session. Use when the active context is becoming long or work must pause without changing client or machine ownership. For an explicit cross-session/client transfer, use $handoff.
code-archaeology
Recover the structure, intent, and lineage of old code, data, or analysis files. Use when inherited or dormant research code must be understood before it is changed. Not for a quality review of already-understood code.
compile-knowledge
Compile literature, meeting notes, session logs, and code findings into a structured per-project knowledge wiki. Use when project evidence is scattered across source records and needs synthesis into durable articles. Not for promoting existing articles into the global vault wiki; use $wiki-grow.
cross-language-check
Replicate a quantitative analysis in a second language (R↔Python↔Stata↔Julia) and compare outputs for implementation errors. Use when an existing empirical result needs independent cross-language verification. Not for reviewing one implementation in place; use $code-suite.
devils-advocate
Adversarially challenge research assumptions, mechanisms, and arguments in writing. Use when stress-testing a claim or design before committing to it. Not for an interactive oral drill or a full referee report; use $grill-me or a review agent.
docs-consistency
Review user-facing documentation for accuracy, consistency, and completeness across private, public, nested repos, and the user manual. Use when docs feel stale, after major changes, or before sharing. (Replaces `repo-doc-audit`)
docx
Create, read, edit, or convert Microsoft Word documents while preserving professional document structure. Use when a .docx file is a primary input or requested output, including tracked changes, comments, images, headings, page furniture, or polished reports and letters. Not for PDFs, spreadsheets, Google Docs, or unrelated coding tasks.
experiment-design
Design empirical studies through power analysis, pre-analysis planning, QSF parsing, and survey architecture. Use when specifying sampling, measurement, treatment, or analysis before data collection. Not for causal identification alone; use $causal-design.
grill-me
Run an interactive one-question-at-a-time oral drill for research defence or active-recall study, escalating around weak answers and ending with a study sheet. Use when the user asks to be grilled, quizzed, or prepared for a viva, job talk, seminar, or exam. Not for a written critique; use $devils-advocate or a review agent.
ideas
Capture and integrate improvement ideas for the shared Claude Code and Codex infrastructure. Use when recording an infrastructure enhancement for later review rather than implementing it immediately.
init-project-course
Bootstrap a university course or module folder with the canonical teaching structure, guidance, and starter files. Use when creating or migrating a course workspace. Not for checking an existing course without modifying it; use $audit-project-course.
init-project-light
Bootstrap a lightweight project with minimal guidance, context, and repository structure. Use when a small non-research project needs durable AI collaboration without the full research or course scaffold. Not for formal research projects; use $init-project-research.
init-project
Bootstrap a new research project. Interview for details, scaffold directory structure, create Overleaf symlink, initialise git, and create project context files.
insights-deck
Archive an exported Claude Code insights HTML report and turn it into a timestamped Beamer presentation usable from either client. Use when the insights export is the source artifact for a presentation. Not for a general research talk; use $talk-deck.
latex-diff
Compare two LaTeX files, project directories, or Git revisions and produce human-readable plus machine-readable severity-graded semantic changes. Use when determining what changed between manuscript versions or preparing a revision audit bundle. Not for proofreading one version; use $proofread.
latex-health-check
Compile all LaTeX projects and report cross-project build consistency. Use when checking whether a collection of papers builds cleanly. Not for rendered visual inspection after a clean build; use $latex-polish.
latex-posters
Create a large-format academic poster in LaTeX using beamerposter, tikzposter, or baposter. Use when the requested deliverable is a conference or research poster rather than sequential presentation slides. For slide decks, use $beamer-deck.
lean-check
Formalize a self-authored lemma or theorem in Lean 4/mathlib and require a clean `lake build` without `sorry`. Use when the mathematical claim can be stated faithfully and machine-checked. For numerical falsification or symbolic algebra, use $numerical-check or $symbolic-check.
math-proof
Write clear, detailed mathematical proofs for academic papers. Use when the user asks to prove a result, derive an equation, justify a claim analytically, or expand a proof sketch into a full proof. Also trigger on "prove", "show analytically", "derive", "justify mathematically", or "write a proof".
mcp-builder
Guide for creating MCP servers that enable LLMs to interact with external services through well-designed tools. Use when building MCP servers to integrate external APIs or services, whether in Python (FastMCP) or Node/TypeScript (MCP SDK).
numerical-check
Numerically stress-test a self-authored mathematical claim over its parameter space to seek counterexamples or characterize violations. Use when checking monotonicity, thresholds, inequalities, comparative statics, or limits computationally. For algebraic proof or Lean formalization, use $symbolic-check or $lean-check.
pipeline-manifest
Build a traceability manifest linking analysis scripts to inputs, outputs, and manuscript figures or tables. Use when documenting a computational pipeline or locating the source of a reported artefact. Not for verifying that paper claims match code outputs; use the code-paper auditor.
playwright-cli
Automate browser interactions and inspect or test web pages through Playwright commands. Use when the task requires deterministic browser navigation, screenshots, selectors, or Playwright-test work. For a full local-webapp test workflow, use $webapp-testing.
postmortem
Deliver a structured post-mortem after incidents, mistakes, or stuck sessions. Use when the user requests a structured post-mortem after incidents, mistakes, or stuck sessions.
pre-commit-audit
Deliver a fast pre-commit safety scan: file size, anonymity (author / affiliation strings in tex/bib), hardcoded secrets, and invisible-Unicode carriers. Use when the user requests a fast pre-commit safety scan: file size, anonymity (author / affiliation strings in tex/bib), hardcoded secrets, and invisible-Unicode carriers. Triggers: 'audit before commit', 'check before push', 'pre-commit scan', 'safety check'.
project-deck
Create a concise presentation deck that communicates a project's current state, decisions, evidence, risks, and next steps. Use when preparing a project update for collaborators, supervisors, or stakeholders. Not for a research talk centered on one paper; use $talk-deck.
project-safety
Install or reconcile research-project safety rules and protected folder boundaries for data, code, outputs, and paper sources. Use when a project lacks guardrails or is being migrated into the governed structure. Not for auditing the full research scaffold; use $audit-project-research.
proof-readability
Improve the exposition and readability of a mathematical proof already verified as correct without changing its mathematics. Use when polishing a lemma, theorem, proof, or appendix after correctness checks. Not for verifying the proof; use $verify-math.
Read, create, combine, split, rotate, OCR, watermark, secure, or extract content from PDF files. Use when a PDF is a primary input or requested output. Not for LaTeX source editing or Word and spreadsheet deliverables.
handoff
Create, accept, or update the persistent `.context/ai-handoff.md` state shared by AI sessions and machines. Use when continuing in a new Claude or Codex session, transferring work between clients, or recording ownership and restart state.
init-project-orchestration
Create or migrate project-level agents, repeatable project workflows, and planning state from one client-neutral contract, then render repository-scoped adapters for both Claude Code and Codex. Use when a research project needs role separation, project commands, formal phase tracking, or conversion from an existing Claude-only .claude/agents and .claude/commands setup.
Bio shown is the top-scored skill's repo description as a fallback — real GitHub bios land in a future update.