Add interactive setup wizard and refactor output handling

[valITino]

Summary

This PR introduces a comprehensive interactive setup wizard (setup.sh) that streamlines the first-time installation experience, alongside a refactoring of output file handling to use host-mounted directories instead of Docker volumes.

Key Changes

New Setup Wizard (setup.sh)

• Interactive installation flow: Guides users through prerequisites checking, environment configuration, optional component selection, and service startup
• Prerequisite validation: Checks for Docker, Docker Compose, Git, and available disk space with helpful error messages
• Non-interactive mode: Supports command-line flags (--api-key, --minimal, --with-neo4j, etc.) for automation
• Health monitoring: Waits for core services to become healthy before declaring setup complete
• User-friendly output: Color-coded messages with progress indicators and actionable next steps

Output File Handling Refactoring

• Host-mounted directories: Replaced Docker volume results with bind mounts:
  • ./output/reports/ → /root/reports/ (pentest reports)
  • ./output/screenshots/ → /tmp/screenshots/ (PoC evidence)
  • ./output/sessions/ → /root/results/ (aggregated session JSONs)
• Direct filesystem access: Users can now access output files directly from their host without docker cp
• Automatic directory creation: setup.sh creates the output directory structure

Documentation Updates

• README.md: Added "Output Files" section, expanded installation instructions with quick-start wizard, updated component table
• DOCKER.md: Clarified Ollama as optional (v2.1+), updated architecture diagrams, simplified usage examples
• .env.example: Reorganized with clear REQUIRED vs OPTIONAL sections, improved comments

Configuration & Build Changes

• docker-compose.yml: Replaced results volume with bind mount for screenshot-mcp, removed unused volume definition
• Makefile: Added setup target as primary installation method
• .gitignore: Added output/ directory and plan.md to ignored paths
• inject_verification.py: Minor code formatting improvement (extracted targets variable)

Container Entrypoint Updates

• claude-code-entrypoint.sh: Updated help text to reference output files mount point

Notable Implementation Details

• The setup wizard uses semantic versioning comparison for Docker/Compose version checks
• Profiles are conditionally applied based on user selections (neo4j, gateway, ollama)
• Health checks specifically wait for kali-mcp and screenshot-mcp core services
• API key input uses read -rsp for secure password-style input
• The wizard gracefully handles existing .env files with user confirmation before overwriting

https://claude.ai/code/session_01JZbXEtmxC7P6HLbTDF2i4j