Complete Setup Walkthrough

Step 1: Install Software (~10 min)

Open PowerShell as Administrator and run all these commands:

# Install all prerequisites (run each line)
winget install Microsoft.PowerShell
winget install OpenJS.NodeJS.LTS
winget install Python.Python.3.11
winget install Git.Git
winget install GitHub.cli

Step 2: Authenticate with GitHub (~5 min)

If you don't have a GitHub account, create one at github.com/signup first.

# Authenticate GitHub CLI (opens browser)
gh auth login

When prompted, select:

• GitHub.com > HTTPS > Login with a web browser

A browser opens - log in and authorize. Then verify:

gh auth status    # Should show "Logged in to github.com"

Step 3: Install & Authenticate Claude (~3 min)

# Install Claude Code CLI
npm install -g @anthropic-ai/claude-code

# First run - opens browser for Anthropic login
cd ~
claude

A browser opens to Anthropic's login page. Log in (or create account), authorize, then return to terminal. Type /exit to quit.

Step 4: Generate GitHub Token (~2 min)

1. Go to github.com/settings/tokens
2. Click "Generate new token (classic)"
3. Name: "Claude Code"
4. Select scopes: repo (full control)
5. Click "Generate token"
6. Copy the token immediately (you won't see it again!)

How to use: Click the copy button on each prompt, paste into Claude, and let it run. Wait for each to complete before moving to the next.

Check my system setup: verify that Node.js, Python, Git, and PowerShell 7 are installed correctly. Show me the version of each.

Configure my git with these settings:
- Name: [REPLACE WITH YOUR NAME]
- Email: [REPLACE WITH YOUR EMAIL]
- Credential helper: manager
- Default branch: main
- Enable LFS
- Set http.postBuffer to 1GB for large files

Create a starter CLAUDE.md file at ~/.claude/CLAUDE.md with these rules:
- Python-first approach (always prefer Python scripts)
- No emoji or Unicode special characters
- Never commit credentials to git
- Windows/PowerShell environment
- Temperature 0 for deterministic output
- Say "I don't know" rather than guess

Update my ~/.claude/settings.json to use the sonnet model with always_thinking enabled.

Create a user-config.json template at ~/.claude/user-config.json for storing my GitHub credentials. Use placeholder values and tell me where to paste my actual token.

Create a global gitignore file at ~/.gitignore_global that excludes .claude/ and CLAUDE.md from all repositories, then configure git to use it.

Install the requests Python package which is needed for the verification tools.

Create a ~/Projects folder, clone the octocat/Hello-World repository into it, and verify the clone worked by showing the contents.

Run a complete setup verification:
1. Check all config files exist (~/.claude/CLAUDE.md, settings.json, user-config.json)
2. Verify git is configured correctly (show user.name, user.email, credential.helper)
3. Confirm global gitignore is set up
4. Show a summary of what's ready and what might need attention

Common Setup Issues

Tips & Tricks for Power Users

First 5 Minutes: Essential Settings

Configure these settings immediately after installation for the best experience:

claude --dangerously-skip-permissions

{
  "alwaysThinkingEnabled": true
}

"Plan first: [your complex task here]"

Prompt Patterns: Magic Words That Work

These phrases trigger specific Claude behaviors:

Workflow Optimization

Python-First Approach

Before doing anything manually, ask: "Can Python do this?"

Context Management

Keep your sessions efficient with these commands:

First Commands After Setup

Run these commands in order when starting with a new project:

/install-github-app
/init
Plan Modus Einschalten

Note: "Plan Modus Einschalten" activates plan mode for complex tasks - Claude will show you the plan before executing.

Cloning Project Repositories

Example for the Implied Risk Premia project:

clone the repo http://github.com/Digital-AI-Finance/implied-risk-premia

Autonomous Execution Mode

For batch tasks, use these trigger phrases:

# Run all tasks without questions
"Execute autonomously: run all chart scripts and fix any errors"

# Complete everything in one go
"Complete without asking: format all Python files and run tests"

# Batch processing
"Run all tasks: generate all PDFs in the slides folder"

Behavior: Claude makes reasonable decisions, runs sequentially, handles errors, reports completion.

Quality Control

Anti-Hallucination Prompts

Prevent Claude from making things up:

Professional Output Rules

Add these to your CLAUDE.md for consistent output:

Quick Reference Card

Claude Code CLI Setup Guide

1. Overview & Prerequisites

What is Claude Code CLI?

Claude Code is Anthropic's official command-line interface for Claude AI. It provides an interactive terminal experience for software engineering tasks, code generation, file manipulation, and complex multi-step workflows.

Prerequisites

Installation

npm install -g @anthropic-ai/claude-code

# Navigate to any project directory
cd C:\path\to\your\project

# Launch Claude Code
claude

claude --version
claude --help

2. Directory Structure (~/.claude/)

After installation, Claude Code creates a configuration directory at C:\Users\{USERNAME}\.claude\ containing all settings, credentials, and tools.

Key Files Summary

3. Global Configuration (CLAUDE.md)

The CLAUDE.md file at ~/.claude/CLAUDE.md contains global instructions that apply to ALL projects. This is the most important configuration file.

Key Rules

project/
+-- 01_concept_name/
|   +-- chart.py      # Single figure, figsize=(10,6)
|   +-- chart.pdf     # Generated output
+-- 02_another_chart/
    +-- chart.py
    +-- chart.pdf

Character Restrictions

Academic Extensions

Additional rules for academic/research workflows:

• Reproducibility: Full pipeline Python scripts with pinned versions
• Chart Style: Matplotlib/Seaborn, grayscale-friendly, B&W print safe
• Beamer: Madrid theme, 8pt font, chart-heavy, minimal bullets
• Citations: BibTeX + natbib, verify ALL citations
• Versioning: YYYYMMDD_HHMM_ prefix for all .tex outputs

4. Settings Configuration (settings.json)

The settings.json file controls model selection, plugins, and IDE behavior.

Current Configuration

{
  "model": "opus",
  "always_thinking": true,
  "statusline": {
    "enabled": true,
    "script": "~/.claude/statusline.ps1"
  },
  "plugins": {
    // All plugins disabled by default
  }
}

Model Options

Status Line

The status line displays context information in the Claude Code interface:

Organization | Email | Directory | Model: opus

Powered by statusline.ps1 which extracts git config, email domain, and current directory.

Plugin Management

50+ plugins available but ALL DISABLED by default for stability. Available plugins include:

• GitHub integration
• Code review tools
• Slack, Vercel, Firebase integrations
• LSP servers (pyright, rust-analyzer, etc.)

5. Git Global Setup

Configure Git for optimal integration with Claude Code and large file handling.

git config --global user.name "Your Name"
git config --global user.email "your.email@example.com"

# Use Git Credential Manager (Windows)
git config --global credential.helper manager

# Increase buffer for large files (1 GB)
git config --global http.postBuffer 1073741824

# Optimize for slow connections
git config --global http.lowSpeedTime 999999

# Install Git LFS
git lfs install

# Track large file types in your repo
git lfs track "*.pdf"
git lfs track "*.xlsx"

# View all global settings
git config --global --list

# Expected output includes:
# user.name=Your Name
# user.email=your.email@example.com
# credential.helper=manager
# http.postbuffer=1073741824

Recommended .gitignore Additions

# Claude Code files (always ignore)
.claude/
CLAUDE.md

# Python
__pycache__/
*.pyc
.venv/

# LaTeX auxiliary files
*.aux
*.log
*.out
*.toc
*.nav
*.snm

6. GitHub CLI (gh) Setup

The GitHub CLI enables seamless interaction with GitHub repositories, issues, and pull requests.

# Via winget (recommended)
winget install GitHub.cli

# Or via Chocolatey
choco install gh

# Verify installation
gh --version

gh auth login

gh auth status

github.com
  - Logged in to github.com as USERNAME
  - Git operations protocol: https
  - Token: ghp_****
  - Token scopes: admin:org, repo, workflow, ...

# Set HTTPS as default protocol
gh config set git_protocol https

# Enable prompts
gh config set prompt enabled

Required Token Scopes

Common GitHub CLI Commands

# Clone a repository
gh repo clone owner/repo

# Create a pull request
gh pr create --title "Title" --body "Description"

# List open issues
gh issue list

# View PR status
gh pr status

# Create a new repo
gh repo create my-repo --private

7. GitLab CLI Setup

For GitLab integration (e.g., git.fhgr.ch), use the python-gitlab CLI.

pip install python-gitlab

[global]
default = fhgr
timeout = 30

[fhgr]
url = https://git.fhgr.ch
private_token = YOUR_GITLAB_TOKEN_HERE
api_version = 4

[gitlab]
url = https://gitlab.com
private_token = YOUR_GITLAB_COM_TOKEN_HERE
api_version = 4

# Check CLI location
where gitlab

# Expected: C:\Users\...\anaconda3\Scripts\gitlab.exe

Common GitLab CLI Commands

# List projects
gitlab project list

# List project pipelines
gitlab project-pipeline list --project-id 123

# List issues
gitlab project-issue list --project-id 123

# List merge requests
gitlab project-merge-request list --project-id 123

# List wiki pages
gitlab project-wiki list --project-id 123

Repository Hierarchy

8. Credential Management

All API tokens and credentials are stored centrally in ~/.claude/user-config.json.

File Structure

{
  "github": {
    "token": "ghp_xxxxxxxxxxxxxxxxxxxx",
    "username": "your-username",
    "organizations": ["Digital-AI-Finance"]
  },
  "gitlab": {
    "fhgr": {
      "token": "glpat-xxxxxxxxxxxxxxxxxxxx",
      "url": "https://git.fhgr.ch",
      "groups": ["digital-finance"]
    }
  },
  "zenodo": {
    "token": "xxxxxxxxxxxxxxxxxxxx",
    "url": "https://zenodo.org"
  },
  "cloudflare": {
    "account_id": "xxxxxxxxxxxxxxxxxxxx",
    "api_token": "xxxxxxxxxxxxxxxxxxxx"
  }
}

Adding New Credentials

1. Open ~/.claude/user-config.json in a text editor
2. Add a new key-value pair following the existing structure
3. Save the file
4. Restart Claude Code to pick up changes

Security Best Practices

Setting File Permissions (Windows)

# PowerShell - restrict to current user only
$path = "$env:USERPROFILE\.claude\user-config.json"
$acl = Get-Acl $path
$acl.SetAccessRuleProtection($true, $false)
$rule = New-Object System.Security.AccessControl.FileSystemAccessRule(
    $env:USERNAME, "FullControl", "Allow"
)
$acl.SetAccessRule($rule)
Set-Acl $path $acl

9. Verification Tools

Custom tools to prevent hallucinations and validate content before finalizing.

9.1 Beamer Validation Suite

Location: ~/.claude/tools/beamer_validation/

Purpose: Validate LaTeX Beamer presentations for errors, broken references, and missing files.

Usage

# Full validation (requires internet)
python ~/.claude/tools/beamer_validation/validate_beamer.py slides.tex

# Quick validation (offline only)
python ~/.claude/tools/beamer_validation/validate_beamer.py slides.tex --quick

# Skip specific checks
python validate_beamer.py slides.tex --skip-urls --skip-citations

Available Checks

9.2 Hallucination Checks Suite

Location: ~/.claude/tools/hallucination_checks/

Code Verification

# Verify Python imports exist on PyPI
python ~/.claude/tools/hallucination_checks/code/verify_imports.py script.py

# Verify npm packages exist
python ~/.claude/tools/hallucination_checks/code/verify_npm.py package.json

# Test regex patterns
python ~/.claude/tools/hallucination_checks/code/verify_regex.py "\d{3}-\d{4}" "123-4567"

Data Verification

# Verify math calculations
python ~/.claude/tools/hallucination_checks/data/verify_calculations.py "sqrt(16) + 2^3" "12"

# Verify statistical claims
python ~/.claude/tools/hallucination_checks/data/verify_statistics.py --data "1,2,3,4,5" --claim "mean=3"

API Verification

# Verify GitHub repo exists
python ~/.claude/tools/hallucination_checks/api/verify_github.py pytorch/pytorch

# Verify arXiv paper ID
python ~/.claude/tools/hallucination_checks/api/verify_arxiv.py 2301.00001

# Verify ORCID
python ~/.claude/tools/hallucination_checks/api/verify_orcid.py 0000-0002-1825-0097

# Search Semantic Scholar
python ~/.claude/tools/hallucination_checks/api/verify_semantic_scholar.py --search "attention is all you need"

# Verify HuggingFace model
python ~/.claude/tools/hallucination_checks/api/verify_huggingface.py --model bert-base-uncased

# Verify ISBN
python ~/.claude/tools/hallucination_checks/api/verify_isbn.py 978-0-13-468599-1

Fact Verification

# Verify Wikipedia article/claim
python ~/.claude/tools/hallucination_checks/facts/verify_wikipedia.py "Alan Turing" --claim "born in 1912"

Output Format

All tools use consistent output prefixes:

[OK]   - Verification passed
[FAIL] - Verification failed
[WARN] - Warning (partial match)
[SKIP] - Check skipped

Dependencies

pip install requests>=2.28.0

10. Templates & Agents

Available Templates

Research Page Template

Location: ~/.claude/templates/research-page-template.md

Generates single-file HTML research project pages with:

• Compact sidebar layout (160px fixed left sidebar)
• OpenAlex integration for publications
• Team member profiles with ORCIDs
• Collaboration tracking
• Responsive design

Academic Primer Template

Location: ~/.claude/templates/academic-primer-template/

Full academic paper scaffold with:

• LaTeX document structure
• Bibliography management
• Figure generation scripts
• GitHub workflows
• Docker configuration

Available Agents

11. Workflow Best Practices

Session Management

# At session start
/init

# When context reaches ~20k tokens remaining
/init then /compact

This ensures continuity and prevents context overflow in long sessions.

Context Management Protocol

1. Run /init at the start of every new session
2. Monitor token usage in the status bar
3. When approaching limit, run /compact to summarize and continue
4. For very long tasks, break into multiple sessions

Todo Tracking

Use the TodoWrite tool to track complex tasks:

# Claude will create todos like:
- [ ] Research existing implementation
- [ ] Design solution
- [ ] Implement changes
- [ ] Write tests
- [ ] Update documentation

Commit Workflow

When committing changes, Claude follows this protocol:

1. git status - Check untracked files
2. git diff - Review changes
3. git log --oneline -5 - Check commit style
4. git add -A - Stage changes
5. git commit -m "message" - Commit with descriptive message
6. git push - Push to remote (only when requested)

Commit Message Format

Short summary of changes (50 chars max)

- Bullet point details if needed
- Another detail

[Generated with Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

12. Troubleshooting

Common Issues

winget install Git.Git
# Or reinstall Git and select "Git Credential Manager" during setup

Debug Logs

Full debug logs are stored at ~/.claude/debug/. Each session creates a UUID-named .txt file with complete logs.

# View recent debug logs
Get-ChildItem ~/.claude/debug/*.txt | Sort-Object LastWriteTime -Descending | Select-Object -First 5

# Clean up old logs (older than 30 days)
Get-ChildItem ~/.claude/debug/*.txt | Where-Object {$_.LastWriteTime -lt (Get-Date).AddDays(-30)} | Remove-Item

Getting Help

• In Claude Code: Type /help
• Report issues: github.com/anthropics/claude-code/issues

Quick Reference - Command Cheatsheet

Claude Code Commands

claude              # Start Claude Code in current directory
claude --version    # Check version
/init               # Initialize session
/compact            # Compact context
/help               # Show help

Git Commands

git status                    # Check working tree status
git diff                      # Show unstaged changes
git add -A                    # Stage all changes
git commit -m "message"       # Commit with message
git push origin main          # Push to remote
git log --oneline -10         # Recent commits

GitHub CLI Commands

gh auth status                # Check authentication
gh repo clone owner/repo      # Clone repository
gh pr create                  # Create pull request
gh pr list                    # List pull requests
gh issue list                 # List issues

GitLab CLI Commands

gitlab project list                              # List projects
gitlab project-pipeline list --project-id ID     # List pipelines
gitlab project-issue list --project-id ID        # List issues
gitlab project-merge-request list --project-id ID # List MRs

Verification Tools

# Beamer validation
python ~/.claude/tools/beamer_validation/validate_beamer.py slides.tex

# Import verification
python ~/.claude/tools/hallucination_checks/code/verify_imports.py script.py

# GitHub verification
python ~/.claude/tools/hallucination_checks/api/verify_github.py owner/repo

# arXiv verification
python ~/.claude/tools/hallucination_checks/api/verify_arxiv.py 2301.00001