Update fundamentals documentation

[goruha]

Description

Revise fundamentals documentation to match new terminology and structure.

Tasks

• Update all terminology to match new API
• Add "Design Principles" section
• Document separation of data transformations
• Explain strategy pattern for modes
• Document congeneric vs general sequences
• Update all code examples
• Create migration guide from old API
• Add troubleshooting section

Dependencies

• Requires: All restructuring phases completed

Related to

Phase 4: Documentation Updates

Acceptance Criteria

• Fundamentals match implementation
• All code examples run without errors
• Migration guide is comprehensive
• Design principles are clearly explained