Add comprehensive equations documentation

Catalog every equation solved by MFC organized by physical model,
including governing PDEs, equations of state, viscous stress, bubble
dynamics, fluid-structure interaction, phase change, chemistry, surface
tension, MHD, IGR, and all numerical methods. Each section references
the activating input parameter, source file paths, and paper citations.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson