Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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…
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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).
Command Claude Code
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…
Command Claude Code
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.
Command Claude Code
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…
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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…
Command Claude Code
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.
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: