doc: comprehensive README update

• Add table of contents for easy navigation
• Add Features section highlighting key capabilities
• Add Architecture diagram showing component relationships
• Add Quick Start section for fast onboarding
• Add dependency table with purpose descriptions
• Add CLI flags table for terminal chat
• Add Project Structure section with file descriptions
• Add Key Components table explaining each module
• Add Available Tools reference table
• Add Running Tests section
• Add Contributing guidelines
• Reorganize existing Security Model content under clearer headings
• Improve overall structure and readability