Comprehensive refactoring: improve code quality, remove dead code, and enhance API

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This PR implements a comprehensive refactoring of the pytmat codebase to address code quality issues, remove technical debt, and improve the user experience while maintaining full backward compatibility.

🔧 Key Improvements

Dead Code Removal

• Eliminated unused TCoefficients and RCoefficients structs (~50 lines of dead code)
• Removed associated methods that were never called
• Fixed broken test function that referenced non-existent add() function
• Resolved all compiler warnings about unused code

Code Organization & Maintainability

• Created optical_math module with reusable mathematical functions:
  • cos_refraction_angle() - Calculate refraction angles using Snell's law
  • fresnel_coefficients() - Compute TE/TM reflection and transmission coefficients
  • propagation_matrix() - Generate layer propagation matrices
  • interface_matrix() - Create interface transfer matrices
• Consolidated duplicate transfer_for_wavelength implementations into single method
• Added meaningful constants (TWO_PI, ONE, ZERO, PARALLEL_THRESHOLD) to eliminate magic numbers
• Improved documentation with comprehensive docstrings

Enhanced Python API

The Python interface now provides both legacy compatibility and modern usability:

import pytmat
import numpy as np

# Enhanced input validation with helpful error messages
data = pytmat.DataPy(d, n, wl, theta, phi)

# New descriptive property names alongside legacy ones
thicknesses = data.layer_thicknesses  # same as data.d
wavelengths = data.wavelengths        # same as data.wl
angle = data.incident_angle          # same as data.theta

# Simulation results with additional computed properties
sim = data.simulate()
reflection = sim.reflection          # same as sim.r
transmission = sim.transmission      # same as sim.t
absorbance = sim.absorbance         # new: 1 - R - T

# Built-in energy conservation validation
is_valid = sim.validate_energy_conservation()
max_error = sim.energy_conservation_error()

Input Validation & Error Handling

• Comprehensive validation of array dimensions and physical constraints
• Descriptive error messages explaining what went wrong and how to fix it
• Checks for positive wavelengths and layer thicknesses
• Validation that incident angle is within physical bounds (0 to π/2)

Performance Optimizations

• Fixed parallel processing to avoid borrowing issues with OnceCell
• Optimized memory allocation patterns by reducing unnecessary clones
• Maintained efficient caching while improving code clarity

🧪 Quality Assurance

• All existing tests continue to pass
• No compiler warnings remain
• Added proper .gitignore to exclude build artifacts
• Maintained full backward compatibility

📈 Impact

This refactoring significantly improves code maintainability and user experience:

• Code Quality: Eliminated 147+ lines of dead code and fixed all warnings
• Maintainability: Better organization and documentation make future changes easier
• User Experience: Enhanced API with validation and descriptive properties
• Performance: Optimized parallel processing for large wavelength arrays
• Reliability: Comprehensive input validation prevents common usage errors

The changes represent best practices in Rust development while preserving the existing API for seamless upgrades.

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