GitHub - Galaxy-Dawn/claude-scholar: Personal AI CLI configuration for academic research & software development. Supports Claude Code, OpenCode, and Codex CLI — covering the full research lifecycle from ideation to publication.

Personal Claude Code / Codex CLI / OpenCode configuration for academic research and software development — covering the full research lifecycle from ideation to publication.

News

2026-02-26: Zotero MCP Web API mode — remote access, import papers via DOI/arXiv ID/URL, collection management, item updates, safe deletion; config guides for Claude Code, Codex CLI, OpenCode
2026-02-25: Codex CLI support — added codex branch supporting OpenAI Codex CLI with config.toml, 40 skills, 14 agents, and sandbox security
2026-02-23: Added setup.sh installer — safe merge into existing ~/.claude, auto-backup settings.json, smart hooks/mcpServers/plugins merge
2026-02-21: OpenCode support — Claude Scholar now supports OpenCode as an alternative CLI; switch to the opencode branch for OpenCode-compatible configuration

View older changelog

2026-02-20: Bilingual config — translated CLAUDE.md to English for international readability; added CLAUDE.zh-CN.md as Chinese backup; Chinese users can switch with cp CLAUDE.zh-CN.md CLAUDE.md
2026-02-15: Zotero MCP integration — added /zotero-review and /zotero-notes commands, updated research-ideation skill with Zotero integration guide, enhanced literature-reviewer agent with Zotero MCP support for automated paper import, collection management, full-text reading, and citation export
2026-02-14: Hooks optimization — restructured security-guard to two-tier system (Block + Confirm), skill-forced-eval now groups skills into 6 categories with silent scan mode, session-start limits display to top 5, session-summary adds 30-day log auto-cleanup, stop-summary shows separate added/modified/deleted counts; removed deprecated shell scripts (lib/common.sh, lib/platform.sh)
2026-02-11: Major update — added 10 new skills (research-ideation, results-analysis, citation-verification, review-response, paper-self-review, post-acceptance, daily-coding, frontend-design, ui-ux-pro-max, web-design-reviewer), 7 new agents, 8 research workflow commands, 2 new rules (security, experiment-reproducibility); restructured CLAUDE.md; 89 files changed
2026-01-26: Rewrote all Hooks to cross-platform Node.js; completely rewrote README; expanded ML paper writing knowledge base; merged PR #1 (cross-platform support)
2026-01-25: Project open-sourced, v1.0.0 released with 25 skills (architecture-design, bug-detective, git-workflow, kaggle-learner, scientific-writing, etc.), 2 agents (paper-miner, kaggle-miner), 30+ commands (including SuperClaude suite), 5 Shell Hooks, and 2 rules (coding-style, agents)

Introduction

Claude Scholar is a personal configuration system for Claude Code CLI, providing rich skills, commands, agents, and hooks optimized for:

Academic Research - Complete research lifecycle: idea generation → experimentation → results analysis → paper writing → review response → conference preparation
Software Development - Git workflows, code review, test-driven development, ML project architecture
Plugin Development - Skill, Command, Agent, Hook development guides with quality assessment
Project Management - Planning documents, code standards, automated workflows with cross-platform hooks

Quick Navigation

Topic	Description
🚀 Quick Start	Get up and running in minutes
📚 Core Workflows	Paper writing, code organization, skill evolution
🛠️ What's Included	Skills, commands, agents overview
📖 Installation Guide	Full, minimal, or selective setup
📦 MCP Setup	Zotero MCP for research workflows
🔧 Project Rules	Coding style and agent orchestration

Core Workflows

Primary Workflows

Complete academic research lifecycle - 7 stages from idea to publication.

1. Research Ideation (Zotero-Integrated)

End-to-end research startup from idea generation to literature management:

Tools: research-ideation skill + literature-reviewer agent + Zotero MCP

Process:

5W1H Brainstorming: What, Why, Who, When, Where, How → structured thinking framework
Literature Search & Import: WebSearch finds papers → extract DOIs → auto-import to Zotero via add_items_by_doi → classify into themed sub-collections (Core Papers, Methods, Applications, Baselines, To-Read)
PDF & Full-Text: find_and_attach_pdfs batch-attaches open-access PDFs → get_item_fulltext reads full paper content for deep analysis (fallback: abstract + domain knowledge)
Gap Analysis: 5 types (Literature, Methodological, Application, Interdisciplinary, Temporal) → identify 2-3 concrete research opportunities
Research Question: SMART principles → formulate specific, measurable questions
Method Selection & Planning: Evaluate method applicability → timeline, milestones, risk assessment

Zotero Collection Structure:

📁 Research-{Topic}-{YYYY-MM}
  ├── 📁 Core Papers
  ├── 📁 Methods
  ├── 📁 Applications
  ├── 📁 Baselines
  └── 📁 To-Read

Output: literature-review.md + research-proposal.md + references.bib (exported from Zotero) + organized Zotero collection with PDFs

Commands:

/research-init "topic" → full workflow: create Zotero collection → search & import papers → full-text analysis → gap analysis → generate review & proposal
/zotero-review "collection" → analyze an existing Zotero collection → generate literature review with comparison matrix
/zotero-notes "collection" → batch read papers → generate structured reading notes (summary/detailed/comparison formats)

2. ML Project Development

Maintainable ML project structure for experiment code:

Tools: architecture-design skill + code-reviewer agent + git-workflow skill

Process:

Structure: Factory & Registry patterns → config-driven models (only cfg parameter) → enforced by rules/coding-style.md
Code Style: 200-400 line files → type hints required → @dataclass(frozen=True) for configs → max 3-level nesting
Debug (bug-detective): Error pattern matching for Python/Bash/JS → stack trace analysis → anti-pattern identification
Git: Conventional Commits (feat/scope: message) → branch strategy (master/develop/feature) → merge with --no-ff

Commands: /plan, /commit, /code-review, /tdd

3. Experiment Analysis

Statistical analysis and visualization of experimental results:

Tools: results-analysis skill + data-analyst agent

Process:

Data Processing: Automated cleaning and preprocessing of experiment logs
Statistical Testing: t-test, ANOVA, Wilcoxon signed-rank → validate significance
Visualization: matplotlib/seaborn integration → publication-ready figures (line plots, bar charts, heatmaps)
Ablation Studies: Systematic component analysis → understand contribution of each part

Command: /analyze-results <experiment_dir> → generates analysis report with figures and statistics

4. Paper Writing

Systematic paper writing from template to final draft:

Tools: ml-paper-writing skill + paper-miner agent + latex-conference-template-organizer skill

Process:

Template Preparation: Download conference .zip → extract main files → remove sample content → clean Overleaf-ready structure
Citation Verification (citation-verification): Multi-layer validation (Format → API → Information → Content) → prevents hallucinations
Systematic Writing: Narrative framing → 5-sentence abstract formula → section-by-section drafting with feedback cycles
Anti-AI Processing (writing-anti-ai): Remove inflated symbolism, promotional language, vague attributions → add human voice and rhythm → bilingual support (EN/CN)

Venues: NeurIPS, ICML, ICLR, ACL, AAAI, COLM, Nature, Science, Cell, PNAS

5. Paper Self-Review

Quality assurance before submission:

Tools: paper-self-review skill

Process:

Structure Check: Logical flow, section balance, narrative coherence
Logic Validation: Argument soundness, claim-evidence alignment, assumption clarity
Citation Audit: Reference accuracy, proper attribution, citation completeness
Figure Quality: Visual clarity, caption completeness, color accessibility
Writing Polish: Grammar, clarity, conciseness, academic tone
Compliance: Page limits, formatting requirements, ethical disclosures

6-item checklist → systematic quality assessment

6. Submission & Rebuttal

Paper submission and review response:

Tools: review-response skill + rebuttal-writer agent

Submission Process:

Pre-submission: Conference-specific checklists (NeurIPS 16-item, ICML Broader Impact, ICLR LLM disclosure)
Format Check: Page limits, anonymization, supplementary materials
Final Review: Proofread, check references, verify figures

Rebuttal Process:

Review Analysis: Parse and classify comments (Major/Minor/Typo/Misunderstanding)
Response Strategy: Accept/Defend/Clarify/Experiment → tailored approach per comment type
Rebuttal Writing: Structured response with evidence and reasoning
Tone Management: Professional, respectful, evidence-based language

Command: /rebuttal <review_file> → generates complete rebuttal document with experiment plan

7. Post-Acceptance Processing

Conference preparation and research promotion:

Tools: post-acceptance skill

Process:

Presentation: Slide creation guidance (15/20/30 min formats) → visual design principles → storytelling structure
Poster: Academic poster templates (A0/A1 sizes) → layout optimization → visual hierarchy
Promotion: Social media content (Twitter/X, LinkedIn) → blog posts → press releases → research summaries

Commands: /presentation, /poster, /promote → automated content generation

Coverage: 90% of academic research lifecycle (from idea to publication)

Supporting Workflows

These workflows run in the background to enhance the primary workflows.

Automated Enforcement Workflow

Cross-platform hooks (Node.js) automate workflow enforcement:

Session Start → Skill Evaluation → Session End → Session Stop

skill-forced-eval (skill-forced-eval.js): Before EVERY user prompt → groups all available skills (local + plugins) into 6 categories → silent scan mode, only outputs matched skills → requires activation before implementation → ensures no relevant skill is missed
session-start (session-start.js): Session begins → displays Git status, pending todos, available commands (top 5 with fold count), package manager → shows project context at a glance
session-summary (session-summary.js): Session ends → generates comprehensive work log → summarizes all changes made → provides smart recommendations for next steps → auto-cleans logs older than 30 days
stop-summary (stop-summary.js): Session stops → quick status check with separate added/modified/deleted counts → groups temp files by folder (top 3 per folder) → shows actionable cleanup suggestions
security-guard (security-guard.js): Two-tier security system — Block tier: immediately rejects catastrophic commands (rm -rf /, dd, mkfs, system dirs); Confirm tier: injects systemMessage forcing model to ask user before executing dangerous-but-legitimate operations (git push --force, git reset --hard, chmod 777, SQL DROP/DELETE/TRUNCATE, sensitive file writes)

Cross-platform: All hooks use Node.js (not shell scripts) ensuring Windows/macOS/Linux compatibility.

Knowledge Extraction Workflow

Two specialized mining agents continuously extract knowledge to improve skills:

paper-miner (agent): Analyze research papers (PDF/DOCX/arXiv links) → extracts writing patterns, structure insights, venue requirements, rebuttal strategies → updates ml-paper-writing/references/knowledge/ with categorized entries (structure.md, writing-techniques.md, submission-guides.md, review-response.md)
kaggle-miner (agent): Study winning Kaggle competition solutions → extract competition briefs, front-runner detailed technical analysis, code templates, best practices → update the kaggle-learner skill's knowledge base (references/knowledge/[domain]/ directories, categorized by NLP/CV/Time Series/Tabular/Multimodal)

Knowledge feedback loop: Each paper or solution analyzed enriches the knowledge base, creating a self-improving system that evolves with your research.

Skill Evolution System

3-step continuous improvement cycle for maintaining and improving skills:

skill-development → skill-quality-reviewer → skill-improver

Develop (skill-development): Create skills with proper YAML frontmatter → clear descriptions with trigger phrases → progressive disclosure (lean SKILL.md, details in references/)
Review (skill-quality-reviewer): 4-dimension quality assessment → Description Quality (25%), Content Organization (30%), Writing Style (20%), Structural Integrity (25%) → generates improvement plan with prioritized fixes
Improve (skill-improver): Merges suggested changes → updates documentation → iterates on feedback → reads improvement plans and applies changes automatically

File Structure

View file structure

claude-scholar/
├── hooks/               # Cross-platform JavaScript hooks (automated enforcement)
│   ├── hook-common.js           # Shared utilities (git diff, change analysis)
│   ├── session-start.js         # Session begin - Git status, todos, top 5 commands
│   ├── skill-forced-eval.js     # Silent scan, 6-category skill grouping
│   ├── session-summary.js       # Session end - work log, 30-day log auto-cleanup
│   ├── stop-summary.js          # Session stop - added/modified/deleted counts, grouped temp files
│   └── security-guard.js        # Two-tier security: Block (catastrophic) + Confirm (dangerous)
│
├── skills/              # 32 specialized skills (domain knowledge + workflows)
│   ├── ml-paper-writing/        # Full paper writing: NeurIPS, ICML, ICLR, ACL, AAAI, COLM
│   │   └── references/
│   │       └── knowledge/        # Extracted patterns from successful papers
│   │       ├── structure.md           # Paper organization patterns
│   │       ├── writing-techniques.md  # Sentence templates, transitions
│   │       ├── submission-guides.md   # Venue requirements (page limits, etc.)
│   │       └── review-response.md     # Rebuttal strategies
│   │
│   ├── research-ideation/        # Research startup: 5W1H, literature review, gap analysis
│   │   └── references/
│   │       ├── 5w1h-framework.md           # Systematic thinking tool
│   │       ├── gap-analysis-guide.md       # 5 types of research gaps
│   │       ├── literature-search-strategies.md
│   │       ├── research-question-formulation.md
│   │       ├── method-selection-guide.md
│   │       └── research-planning.md
│   │
│   ├── results-analysis/         # Experiment analysis: statistics, visualization, ablation
│   │   └── references/
│   │       ├── statistical-methods.md      # t-test, ANOVA, Wilcoxon
│   │       ├── visualization-best-practices.md  # matplotlib/seaborn
│   │       ├── results-writing-guide.md    # Writing results sections
│   │       └── common-pitfalls.md          # Common analysis mistakes
│   │
│   ├── review-response/          # Systematic rebuttal writing
│   │   └── references/
│   │       ├── review-classification.md    # Major/Minor/Typo/Misunderstanding
│   │       ├── response-strategies.md      # Accept/Defend/Clarify/Experiment
│   │       ├── rebuttal-templates.md       # Structured response templates
│   │       └── tone-guidelines.md          # Professional language
│   │
│   ├── paper-self-review/        # 6-item quality checklist
│   ├── post-acceptance/          # Conference preparation
│   │   └── references/
│   │       ├── presentation-templates/     # Slide creation (15/20/30 min)
│   │       ├── poster-templates/           # Academic poster design
│   │       ├── promotion-examples/         # Social media content
│   │       └── design-guidelines.md        # Visual design principles
│   │
│   ├── citation-verification/    # Multi-layer citation validation
│   ├── writing-anti-ai/         # Remove AI patterns: symbolism, promotional language
│   │   └── references/
│   │       ├── patterns-english.md    # English AI patterns to remove
│   │       └── patterns-chinese.md     # Chinese AI patterns to remove
│   │
│   ├── architecture-design/     # ML project patterns: Factory, Registry, Config-driven
│   ├── git-workflow/            # Git discipline: Conventional Commits, branching
│   ├── bug-detective/           # Debugging: Python, Bash, JS/TS error patterns
│   ├── code-review-excellence/  # Code review: security, performance, maintainability
│   ├── skill-development/       # Skill creation: YAML, progressive disclosure
│   ├── skill-quality-reviewer/  # Skill assessment: 4-dimension scoring
│   ├── skill-improver/          # Skill evolution: merge improvements
│   ├── kaggle-learner/          # Learn from Kaggle winning solutions
│   ├── doc-coauthoring/         # Document collaboration workflow
│   ├── latex-conference-template-organizer  # Template cleanup for Overleaf
│   └── ... (10+ more skills)
│
├── commands/            # 50+ slash commands (quick workflow execution)
│   ├── research-init.md         # Launch research startup workflow
│   ├── zotero-review.md         # Read Zotero papers, generate literature review
│   ├── zotero-notes.md          # Batch read Zotero papers, generate reading notes
│   ├── analyze-results.md       # Analyze experiment results
│   ├── rebuttal.md              # Generate systematic rebuttal document
│   ├── presentation.md          # Create conference presentation outline
│   ├── poster.md                # Generate academic poster design plan
│   ├── promote.md               # Generate promotion content
│   ├── plan.md                  # Implementation planning with agent delegation
│   ├── commit.md                # Conventional Commits: feat/fix/docs/refactor
│   ├── code-review.md           # Quality and security review workflow
│   ├── tdd.md                   # Test-driven development: Red-Green-Refactor
│   ├── build-fix.md             # Fix build errors automatically
│   ├── verify.md                # Run verification loops
│   ├── checkpoint.md            # Save verification state
│   ├── refactor-clean.md        # Remove dead code
│   ├── learn.md                 # Extract patterns from code
│   ├── update-github.md         # Commit and push to GitHub
│   ├── update-readme.md         # Update README documentation
│   ├── update-memory.md         # Check and update CLAUDE.md memory
│   ├── create_project.md        # Create new project from template
│   ├── setup-pm.md              # Configure package manager (uv/pnpm)
│   └── sc/                      # SuperClaude command suite (30 commands)
│       ├── sc-agent.md           # Agent management
│       ├── sc-estimate.md       # Development time estimation
│       ├── sc-improve.md         # Code improvement
│       └── ...
│
├── agents/              # 14 specialized agents (focused task delegation)
│   ├── literature-reviewer.md   # Literature search and trend analysis
│   ├── data-analyst.md          # Automated data analysis and visualization
│   ├── rebuttal-writer.md       # Systematic rebuttal writing
│   ├── paper-miner.md           # Extract paper knowledge: structure, techniques
│   ├── architect.md             # System design: architecture decisions
│   ├── code-reviewer.md         # Review code: quality, security, best practices
│   ├── tdd-guide.md             # Guide TDD: test-first development
│   ├── kaggle-miner.md          # Extract engineering practices from Kaggle
│   ├── build-error-resolver.md  # Fix build errors: analyze and resolve
│   ├── refactor-cleaner.md      # Remove dead code: detect and cleanup
│   ├── bug-analyzer.md          # Deep code execution flow analysis and root cause investigation
│   ├── dev-planner.md           # Implementation planning and task breakdown
│   ├── ui-sketcher.md           # UI blueprint design and interaction specs
│   └── story-generator.md       # User story and requirement generation
│
├── rules/               # Global guidelines (always-follow constraints)
│   ├── coding-style.md          # ML project standards: file size, immutability, types
│   ├── agents.md                # Agent orchestration: when to delegate, parallel execution
│   ├── security.md              # Secrets management, sensitive file protection
│   └── experiment-reproducibility.md  # Random seeds, config recording, checkpoints
│
├── CLAUDE.md            # Global configuration: project overview, preferences, rules
│
└── README.md            # This file - overview, installation, features

Feature Highlights

Skills (32 total)

Web Design:

frontend-design - Create distinctive, production-grade frontend interfaces
ui-ux-pro-max - UI/UX design intelligence (50+ styles, 97 palettes, 9 stacks)
web-design-reviewer - Visual inspection and design issue fixing

Writing & Academic:

ml-paper-writing - Full paper writing guidance for top conferences/journals
writing-anti-ai - Remove AI writing patterns (bilingual support)
doc-coauthoring - Structured document collaboration workflow
latex-conference-template-organizer - LaTeX template management
daily-paper-generator - Automated daily paper generation for research tracking

Research Workflow:

research-ideation - Research startup: 5W1H brainstorming, literature review, gap analysis
results-analysis - Experiment analysis: statistical testing, visualization, ablation studies
review-response - Systematic rebuttal writing with tone management
paper-self-review - 6-item quality checklist for paper self-assessment
post-acceptance - Conference preparation: presentations, posters, promotion
citation-verification - Multi-layer citation validation to prevent hallucinations

Development:

daily-coding - Daily coding checklist (minimal, auto-triggered)
git-workflow - Git best practices (Conventional Commits, branching)
code-review-excellence - Code review guidelines
bug-detective - Debugging for Python, Bash, JS/TS
architecture-design - ML project design patterns
verification-loop - Testing and validation

Plugin Development:

skill-development - Skill creation guide
skill-improver - Skill improvement tools
skill-quality-reviewer - Quality assessment
command-development - Slash command creation
agent-identifier - Agent configuration
hook-development - Hook development guide
mcp-integration - MCP server integration

Utilities:

uv-package-manager - Modern Python package management
planning-with-files - Markdown-based planning
webapp-testing - Local web application testing
kaggle-learner - Learn from Kaggle solutions

Commands (50+)

Research Commands:

Command	Purpose
`/research-init`	Launch research startup workflow (5W1H, literature review, gap analysis)
`/zotero-review`	Read papers from Zotero collection, generate structured literature review
`/zotero-notes`	Batch read Zotero papers, generate structured reading notes
`/analyze-results`	Analyze experiment results (statistics, visualization, ablation)
`/rebuttal`	Generate systematic rebuttal document from review comments
`/presentation`	Create conference presentation outline
`/poster`	Generate academic poster design plan
`/promote`	Generate promotion content (Twitter, LinkedIn, blog)

Development Commands:

Command	Purpose
`/plan`	Create implementation plans
`/commit`	Commit with Conventional Commits
`/update-github`	Commit and push to GitHub
`/update-readme`	Update README documentation
`/update-memory`	Check and update CLAUDE.md memory
`/code-review`	Perform code review
`/tdd`	Test-driven development workflow
`/build-fix`	Fix build errors
`/verify`	Verify changes
`/checkpoint`	Create checkpoints
`/refactor-clean`	Refactor and cleanup
`/learn`	Extract reusable patterns
`/create_project`	Create new project from template
`/setup-pm`	Configure package manager (uv/pnpm)
`/sc`	SuperClaude command suite (30 commands)

Agents (14 specialized)

Research Agents:

literature-reviewer - Literature search, classification, and trend analysis
data-analyst - Automated data analysis and visualization
rebuttal-writer - Systematic rebuttal writing with tone optimization
paper-miner - Extract paper writing knowledge from successful publications

Development Agents:

architect - System architecture design
build-error-resolver - Fix build errors
code-reviewer - Review code quality
refactor-cleaner - Remove dead code
tdd-guide - Guide TDD workflow
kaggle-miner - Extract Kaggle engineering practices
bug-analyzer - Deep code execution flow analysis and root cause investigation
dev-planner - Implementation planning and task breakdown

Design & Content Agents:

ui-sketcher - UI blueprint design and interaction specs
story-generator - User story and requirement generation

Quick Start

Installation Options

Choose the installation method that fits your needs:

Option 1: Full Installation (Recommended)

git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar
bash /tmp/claude-scholar/scripts/setup.sh

The script merges skills/commands/agents/rules/hooks into your existing ~/.claude, and adds hooks/mcpServers/enabledPlugins to your settings.json (auto-backup to settings.json.bak). Your env and permissions are untouched.

Includes: All 32 skills, 50+ commands, 14 agents, 5 hooks, and project rules.

Option 2: Minimal Installation

Core hooks and essential skills only (faster load, less complexity):

# Clone repository
git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar

# Copy only hooks and core skills
mkdir -p ~/.claude/hooks ~/.claude/skills
cp /tmp/claude-scholar/hooks/*.js ~/.claude/hooks/
cp -r /tmp/claude-scholar/skills/ml-paper-writing ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/research-ideation ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/results-analysis ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/review-response ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/writing-anti-ai ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/git-workflow ~/.claude/skills/
cp -r /tmp/claude-scholar/skills/bug-detective ~/.claude/skills/

# Cleanup
rm -rf /tmp/claude-scholar

Post-install: Merge hooks config into your settings.json — see settings.json.template for the required hooks entries.

Includes: 5 hooks, 7 core skills (complete research workflow + essential development).

Option 3: Selective Installation

Pick and choose specific components:

# Clone repository
git clone https://github.com/Galaxy-Dawn/claude-scholar.git /tmp/claude-scholar
cd /tmp/claude-scholar

# Copy what you need, for example:
# - Hooks only
cp hooks/*.js ~/.claude/hooks/

# - Specific skills
cp -r skills/latex-conference-template-organizer ~/.claude/skills/
cp -r skills/architecture-design ~/.claude/skills/

# - Specific agents
cp agents/paper-miner.md ~/.claude/agents/

# - Project rules
cp rules/coding-style.md ~/.claude/rules/
cp rules/agents.md ~/.claude/rules/

Post-install: Merge hooks config into your settings.json — see settings.json.template.

Recommended for: Advanced users who want custom configurations.

Requirements

Claude Code CLI
Git
Node.js (required for hooks)
uv, Python (for Python development)
Zotero (for Zotero MCP features)

MCP Setup

For Zotero-integrated research workflows, install the MCP server:

# Install from Galaxy-Dawn fork (Web API mode)
uv tool install git+https://github.com/Galaxy-Dawn/zotero-mcp.git

Then add to your ~/.claude/settings.json:

{
  "mcpServers": {
    "zotero": {
      "command": "zotero-mcp",
      "args": ["serve"],
      "env": {
        "ZOTERO_API_KEY": "your-api-key",
        "ZOTERO_LIBRARY_ID": "your-library-id",
        "ZOTERO_LIBRARY_TYPE": "user",
        "UNPAYWALL_EMAIL": "your-email@example.com",
        "UNSAFE_OPERATIONS": "all"
      }
    }
  }
}

See MCP_SETUP.md for detailed setup guide and troubleshooting.

First Run

After installation, the hooks provide automated workflow assistance:

Every prompt triggers skill-forced-eval → ensures applicable skills are considered
Session starts with session-start → displays project context
Sessions end with session-summary → generates work log with recommendations
Session stops with stop-summary → provides status check

Project Rules

Coding Style

Enforced by rules/coding-style.md:

File Size: 200-400 lines maximum
Immutability: Use @dataclass(frozen=True) for configs
Type Hints: Required for all functions
Patterns: Factory & Registry for all modules
Config-Driven: Models accept only cfg parameter

Agent Orchestration

Defined in rules/agents.md:

Available agent types and purposes
Parallel task execution
Multi-perspective analysis

Security

Defined in rules/security.md:

Secrets management (environment variables, .env files)
Sensitive file protection (never commit tokens, keys, credentials)
Pre-commit security checks via hooks

Experiment Reproducibility

Defined in rules/experiment-reproducibility.md:

Random seed management for reproducibility
Configuration recording (Hydra auto-save)
Environment recording and checkpoint management

Contributing

This is a personal configuration, but you're welcome to:

Fork and adapt for your own research
Submit issues for bugs
Suggest improvements via issues

License

MIT License

Acknowledgments

Built with Claude Code CLI and enhanced by the open-source community.

References

This project is inspired by and builds upon excellent work from the community:

everything-claude-code - Comprehensive resource for Claude Code CLI
AI-research-SKILLs - Research-focused skills and configurations

These projects provided valuable insights and foundations for the research-oriented features in Claude Scholar.

For data science, AI research, and academic writing.

Repository: https://github.com/Galaxy-Dawn/claude-scholar

Name		Name	Last commit message	Last commit date
Latest commit History 83 Commits
agents		agents
commands		commands
hooks		hooks
plugins		plugins
rules		rules
scripts		scripts
skills		skills
utils		utils
.gitattributes		.gitattributes
.gitignore		.gitignore
CLAUDE.md		CLAUDE.md
CLAUDE.zh-CN.md		CLAUDE.zh-CN.md
LOGO.png		LOGO.png
MCP_SETUP.md		MCP_SETUP.md
MCP_SETUP.zh-CN.md		MCP_SETUP.zh-CN.md
README.md		README.md
README.zh-CN.md		README.zh-CN.md
settings.json.template		settings.json.template

Galaxy-Dawn/claude-scholar

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Introduction

Quick Navigation

Core Workflows

Primary Workflows

1. Research Ideation (Zotero-Integrated)

2. ML Project Development

3. Experiment Analysis

4. Paper Writing

5. Paper Self-Review

6. Submission & Rebuttal

7. Post-Acceptance Processing

Supporting Workflows

Automated Enforcement Workflow

Knowledge Extraction Workflow

Skill Evolution System

File Structure

Feature Highlights

Skills (32 total)

Commands (50+)

Agents (14 specialized)

Quick Start

Installation Options

Option 1: Full Installation (Recommended)

Option 2: Minimal Installation

Option 3: Selective Installation

Requirements

MCP Setup

First Run

Project Rules

Coding Style

Agent Orchestration

Security

Experiment Reproducibility

Contributing

License

Acknowledgments

References

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