[MDPA] Improve support for Kratos Multiphysics mdpa support

[loumalouomega]

This Pull Request significantly expands and robustifies the support for the Kratos Multiphysics MDPA format. It transforms the MDPA module from a basic reader/writer into a comprehensive tool capable of handling complex simulation setups with high fidelity.

Key Enhancements

1. Expanded Entity Mapping

• Implemented specialized mapping dictionaries for Kratos Geometries, Elements, and Conditions.
• Added support for a wide range of standard Kratos types (e.g., Element3D4N, Element2D3N, SurfaceCondition3D3N, LineCondition2D2N).
• Improved type identification logic to prioritize exact matches and handle legacy/common naming conventions robustly.

2. High-Fidelity Round-Trips via misc_data

• Utilized mesh.misc_data to preserve MDPA-specific metadata that doesn't fit the standard meshio model:
  • Original IDs: Preserves original Kratos IDs for nodes, elements, conditions, and geometries.
  • SubModelParts: Maintains the full hierarchical structure of SubModelParts, including their local data and tables.
  • Mesh Blocks: Supports multi-level solver mesh representations.
• The writer now prioritizes this metadata, allowing for near-identical reconstruction of MDPA files.

3. Hierarchical SubModelPart Support

• Completely refactored the SubModelPart parser to correctly handle nested Begin/End blocks.
• The writer now reconstructs the hierarchical tree structure in the output file, ensuring compatibility with Kratos's model part hierarchy.

4. Corrected Node Ordering (Permutations)

• Fixed node index permutations for higher-order elements (hexahedron20 and hexahedron27).
• Correctly converts between Kratos-specific ordering and meshio's standard VTK-based ordering during both read and write operations.

5. Robust Parser Improvements

• Enhanced block parsing to handle tab characters and comments in headers (e.g., Begin Elements Element3D4N // comment).
• Improved error handling and warnings for malformed or unsupported blocks.

Testing Improvements

• Increased Coverage: Added a comprehensive suite of new tests covering:
  • Elemental and conditional data blocks.
  • Hierarchical SubModelPart round-trips.
  • Higher-order element permutations.
  • Geometries and complex mesh block structures.
• Reference Meshes: Included several new reference .mdpa files in tests/meshes/mdpa/ to verify real-world scenarios.
• Standardized Naming: Renamed test files to follow the project's test_*.mdpa convention.

Code Quality

• Applied isort and black styling to all modified files.
• Resolved all relevant flake8 linting issues.
• Optimized internal helper functions with enhanced inline documentation.

[loumalouomega]

Looks like some tests in the main are failing, I will try to fix them, and cherry-pick in an independent branch

[loumalouomega]

Includes #1554

[loumalouomega]

Okay, now passes