Add additional permission commands for cognitive agent scripts

Implement complete cognitive agent with MCP integration and metacognitive patterns

Refactor code structure for improved readability and maintainability

Updates

Code updates, preparing for course

Major code updates, changes, bonus sections and presentation added

Chapter 5 complete

Chapter 4 complete

New exercises for chapter 4, partial

Updates to code for chapters 2 and 3

chapter 2 examples complete

first push

Initial commit