Update API reference documentation

[goruha]

Description

Regenerate and update API reference documentation to reflect new module structure.

Tasks

• Regenerate API docs from new module structure
• Add module-level docstrings explaining purpose and scope
• Document relationship between modules
• Add typical usage patterns for each module
• Create architecture diagram showing module relationships
• Add transformation pipeline diagram
• Update all code examples

Dependencies

• Requires: All restructuring phases completed

Related to

Phase 4: Documentation Updates

Acceptance Criteria

• API docs reflect current structure
• Architecture is clearly documented
• All examples are correct and tested
• Navigation is intuitive