Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows
This repository also configures its own agents. See what flonat-research tells them →
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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…
Command Claude Code
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.
Command Claude Code
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".
Command Claude Code
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).
Command Claude Code
Manage old recordings — find large files, archive old meetings, delete processed originals. Use when the user says "clean up recordings", "how much space are meetings using", "delete old recordings", "archive meetings", "manage meeting storage", or asks about disk space from minutes.
Command Claude Code
Post-meeting debrief — analyzes what happened, compares outcomes to your prep intentions, tracks decision evolution. Use when the user says "debrief", "what just happened in that meeting", "what did we decide", "debrief that call", "post-meeting", "what changed", or right after stopping a recording.
Command Claude Code
List recent meetings and voice memos. Use when the user asks "what meetings did I have", "show my recent recordings", "any meetings today", "list my voice memos", or wants an overview of their meeting history. Also use when they need to find a specific meeting by browsing rather than searching.
Command Claude Code
Interactive meeting preparation — builds a relationship brief and talking points before a call. Use when the user says "prep me for my call with", "I'm meeting with X", "prepare me for", "what should I bring up with", "meeting prep", "get ready for my call", or wants to review history with someone before a meeting.
Command Claude Code
Generate a daily digest of today's meetings and voice memos — key decisions, action items, and themes across all recordings. Use when the user asks "recap my day", "what happened in my meetings today", "daily summary", "what did I discuss today", "any action items from today", or wants a consolidated view of the day's…
Command Claude Code
Search meeting transcripts and voice memos for people, topics, decisions, commitments, or remembered ideas. Use when the user asks what was discussed, decided, or said across their meeting history. Not for preparing an upcoming meeting; use $meetings-prep.
Command Claude Code
Weekly meeting synthesis — themes, decision arcs, stale commitments, and what deserves your attention next week. Use when the user says "weekly review", "what happened this week", "weekly summary", "recap my week", "any outstanding items", "week in review", or at the end of a work week.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
Command Claude Code
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.
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: