docs: Add natural language explanations to all code examples in PIPELINE.md

Enhanced all code examples with comprehensive documentation comments that explain:
- Mathematical formulas and algorithms
- Parameter meanings and constraints
- Properties captured by specifications
- Relationship to NumPy behavior

This makes the pipeline documentation more accessible and provides clear
guidance for generating well-documented specifications.

🤖 Generated with [Claude Code](https://claude.ai/code)

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

Author: htlou