A community-driven registry for the Claude Code ecosystem. Not affiliated with Anthropic.
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Shareable Claude Code infrastructure for PhD researchers — 48 slash commands, literature search
Made by a humble PhD student. A complete Claude Code infrastructure for researchers — skills, agents, hooks, and rules for academic workflows. Built for researchers who write papers in LaTeX, manage bibliographies, run experiments, and want AI assistance that understands academic conventions.
Works on macOS, Linux, and Windows. Use Claude Code from the terminal CLI, VS Code, JetBrains IDEs, the web, or the desktop app — all share the same skills, agents, and rules.
npx flonat-research
This downloads the package and runs the setup script, which symlinks skills, agents, hooks, and rules into ~/.claude/.
git clone https://github.com/flonat/claude-research.git
cd claude-research
./scripts/setup.sh
git clone https://github.com/flonat/claude-research.git
cd claude-research
.\scripts\setup.ps1
The git clone gives you a local copy you can fully customise — edit .context/profile.md, CLAUDE.md, and workflows to match your research.
# macOS/Linux: pull latest, then re-link without overwriting settings
git pull && ./scripts/setup.sh --update
# Windows (PowerShell):
git pull; .\scripts\setup.ps1 -Update
Then customise .context/profile.md, .context/current-focus.md, and CLAUDE.md with your details. See docs/getting-started.md for the full guide (includes Windows-specific setup, Python install, and troubleshooting).
| Package | Install | Description |
|---|---|---|
llm-council | pip install llm-council | Multi-model council via OpenRouter API |
cli-council | pip install cli-council | Multi-model council via local CLI tools |
| Component | Count | Description |
|---|---|---|
| Skills | 50 | Slash commands for common tasks (/proofread, /latex-autofix, /literature, etc.) |
| Agents | 15 | Specialised reviewers (peer review, referee 2, paper critic, domain review, fixer) |
| Hooks | 9 | Automated guardrails (destructive git protection, context monitoring, etc.) |
| Rules | 18 | Always-on policies (plan before implementing, scope discipline, etc.) |
| Context library | — | Structured files that give Claude persistent memory across sessions |
| Notion integration | — | Task management and research pipeline tracking — setup guide |
| Bibliography MCP | — | Multi-source scholarly search (OpenAlex + Scopus + WoS) — setup guide |
| Council mode | — | Multi-model deliberation (3 reviewers + synthesis) — setup guide |
| CLI tools | — | Notion task management from the terminal — docs |
┌──────────────────────────────────────────────────────────────┐
│ Claude Code (Terminal) Claude Desktop (GUI) │
│ │ │ │
│ CLAUDE.md + Rules MCP Server (load-context) │
│ │ │ │
│ ┌────┴──────────────┬──────────────┐ │ │
│ │ │ │ │ │
│ Context ◄───────── Skills ◄──────┼─────┘ │
│ Library │ │ │
│ CLI Scripts Research Vault │
│ │
│ MEMORY.md ◄─────── Hooks & │
│ + Logs Permissions │
└──────────────────────────────────────────────────────────────┘
The MCP server's load-context tool gives Claude Desktop access to the context library and MEMORY.md — the same files Claude Code reads automatically.
Context Library (.context/) — Markdown files that give Claude persistent memory about you, your projects, and your workflows. Instead of re-explaining your research every session, Claude reads these files automatically.
Skills (skills/) — Slash commands invoked with /<skill-name> or natural language.
50 skills available. Key examples: /proofread, /literature, /bib-validate, /init-project-research, /pre-submission-report, and more.
See docs/skills.md for the full catalogue.
Agents (.claude/agents/) — Specialised personas for complex review tasks, spawning sub-agents for parallel work.
| Agent | Use case |
|---|---|
artifact-coherence-auditor | Audits coherence between paper prose and replication outputs — catches hallucinated results, missing scripts, mismatched numbers, and unverifiable claims |
blindspot | Peripheral vision audit for empirical output |
claim-verify | Verify that cited claims in a paper accurately represent what the source papers actually say |
code-paper-auditor | Use this agent when you need to verify code-paper consistency — mapping every quantitative claim in a paper to its source code and output files |
code-review | Multi-persona orchestrator for adversarial review of R, Python, Julia, or Stata research scripts |
codex-research | Code review and research agent that delegates to OpenAI Codex CLI in headless mode |
domain-reviewer | Research-focused substantive correctness agent |
fatal-error-check | Fast pre-review check for fatal errors in LaTeX papers |
fixer | Generic fix implementer for any critic report |
gemini-research | Web research agent that delegates to Gemini CLI in headless mode |
paper-critic | Adversarial auditor for LaTeX papers |
peer-reviewer | Use this agent when you need to review someone else's paper — as a peer reviewer, discussant, or for reading group preparation |
proposal-reviewer | Use this agent when you need to review a research proposal, extended abstract, conference submission outline, or pre-paper plan — either his own or someone else's |
referee2-reviewer | Use this agent when the user wants a rigorous, adversarial academic review of their work — including papers, manuscripts, research designs, code, or arguments |
reproducibility-auditor | Reviews research workflows for reproducibility gaps — hidden dependencies, absolute paths, undocumented prerequisites, environment assumptions, and output traceability |
See docs/agents.md for detailed descriptions.
Hooks (hooks/) — Automated guardrails that run at specific points in a session.
| Hook | Trigger | What it does |
|---|---|---|
block-destructive-git.sh | Before Bash | catches dangerous git/shell commands |
context-monitor.py | After tool use | tracks tool call count as a heuristic for context usage |
handoff-read.sh | SessionStart | if handoff.md exists in cwd, read it into additionalContext |
postcompact-restore.py | After compact | restores state after context compression |
precompact-autosave.py | Before compact | saves state before context compression |
promise-checker.sh | Session stop | catches "performative compliance": Claude says it remembered/noted/saved |
protect-source-files.sh | Before edit/write | prompts confirmation for files outside |
resume-context-loader.sh | Session resume | surfaces current focus and latest session log |
startup-context-loader.sh | Session start | auto-detects and surfaces project documentation |
See docs/hooks.md for full documentation.
Rules (.claude/rules/) — Always-on policies enforcing good research practices. See docs/rules.md.
Research Vault — Obsidian-style markdown vault (~/Research-Vault) for tasks, pipeline, submissions, venues, people, and themes. Accessed via the taskflow MCP server.
Biblio MCP — Multi-source scholarly search server (OpenAlex + optional Scopus & Web of Science). See docs/bibliography-setup.md.
Flonat-Papers MCP — Zotero library management server (search, PDF extraction, semantic retrieval, BibTeX export). Lives in packages/flonat-papers/ with bundled bib-validate and bib-parse skills.
Council Mode — Multi-model deliberation with 3 LLM providers, anonymised cross-review, and chairman synthesis. See docs/council-mode.md.
| Command | What happens |
|---|---|
| "Plan my day" | Reads context, queries vault, asks questions, creates Must Do / Should Do / Could Do plan |
| "Extract actions from my meeting with [name]" | Finds transcript, extracts tasks with full context, creates in vault |
| "Weekly review" | 4-part reflection: clear the decks, review, plan, project check |
| "What's overdue?" | Queries vault and summarises |
| "Proofread my paper" | 7-category academic check (report only) |
| "Validate my bibliography" | Cross-references \cite{} keys against .bib |
Each session builds on previous ones:
current-focus.md — updated at session end with progress and next stepslog/ — timestamped session logslog/plans/ — saved implementation plansMEMORY.md — accumulated [LEARN] tags (notation, citation, code, method, domain corrections)The recovery protocol reads the latest plan, session log, and current focus to resume seamlessly.
claude-research/
├── CLAUDE.md # Main instruction file (customise this)
├── README.md # This file
├── MEMORY.md # Accumulated knowledge (auto-populated)
├── .claude/
│ ├── agents/ # 15 specialised review agents
│ ├── rules/ # 18 auto-loaded policy rules
│ └── settings.json # Permissions, hooks, model config
├── skills/ # 50 slash commands
│ ├── shared/ # Shared utilities (palettes, scoring, rhetoric)
│ ├── proofread/ # Academic proofreading
│ ├── latex-autofix/ # LaTeX compilation + auto-fix
│ ├── literature/ # Literature search + synthesis
│ └── ... # See docs/components/skills.md for full list
├── hooks/ # 9 automated guardrails
├── .context/ # AI context library
│ ├── profile.md # Your identity and background
│ ├── current-focus.md # What you're working on NOW
│ ├── projects/ # Project metadata
│ ├── preferences/ # Workflow preferences
│ ├── workflows/ # Process guides (daily review, etc.)
│ └── resources/ # Reference data (journal rankings, etc.)
├── .scripts/ # CLI tools for Notion task management
├── packages/
│ ├── cli-council/ # cli-council
│ ├── council-api/ # Multi-model council via OpenRouter API
│ ├── council-cli/ # Multi-model council via local CLI tools
│ ├── mcp-scholarly/ # mcp-scholarly
│ └── scholarly/ # Multi-source scholarly search MCP (OpenAlex + Scopus + WoS)
├── docs/ # Component documentation
├── log/ # Session logs (auto-created)
└── scripts/
└── setup.sh # Initial setup script
| Tool | Why you need it | macOS | Linux | Windows |
|---|---|---|---|---|
| Claude Code | The AI engine — runs skills, agents, hooks | curl -fsSL https://claude.ai/install.sh | bash | same | winget install Anthropic.ClaudeCode |
| Python 3.11+ | Hooks and MCP servers | brew install python@3.12 | apt install python3.12 | winget install Python.Python.3.12 |
| uv | Fast Python package manager — isolates dependencies, replaces pip | brew install uv | curl -LsSf https://astral.sh/uv/install.sh | sh | winget install astral-sh.uv |
| Git | Version control | Included | apt install git | winget install Git.Git |
| TeX Live | LaTeX compilation (/proofread, /latex-autofix) | brew install --cask mactex | apt install texlive-full | install guide |
Also available as a VS Code extension, JetBrains plugin, web app, or desktop app.
See docs/getting-started.md for Fedora/Arch commands, Windows-specific setup, Python version guidance, and troubleshooting.
This infrastructure draws on design patterns from several open-source workflows.
System created January 2026.
MIT
ML engineering — model training, deployment, MLOps, monitoring
DevOps practices — CI/CD, containers, monitoring, infrastructure automation
Professional skills marketplace with production-ready skills for enhanced development
Self-learning system that captures corrections and syncs them to CLAUDE.md and AGENTS.md
