Add multi-compartment (cBNGL) support to NFsim

[akutuva21]

Add Multi-Compartment (cBNGL) Support to NFsim

This PR adds native support for multi-compartment (cBNGL) models to NFsim, enabling molecule transport between compartments. Previously, NFsim only supported well-mixed (single-compartment) simulations.

Key Features

• New Compartment Class: Added compartment.hh/cpp to manage compartment hierarchies and properties.
• Molecule Transport: Implemented MoveTransformation to handle the transport of molecules matching specific patterns between compartments.
• XML Support: Added XML parsing for the <ChangeCompartment> operation, enabling full compatibility with cBNGL models exported from BioNetGen.
• Improved Integration: Updated System and Molecule classes to correctly track and manage compartment assignments during a simulation.

Technical Details

• Core: Added getCompartmentId() to Molecule and TemplateMolecule.
• Destruction: Fixed destructor syntax in system.cpp and added compartment cleanup.
• Input: Updated NFinput.cpp to parse compartment definitions and set up parent-child relationships correctly.

Verification

The implementation has been verified through:

1. WASM Integration: Successfully bundled and tested in a BioNetGen web simulator using Playwright.
2. Native Build: Successfully compiled as a native binary (MinGW/CMake) and verified using BNG2.pl.
3. Parity Tests: Confirmed results match analytical solutions and standard BNGL ODE/SSA engines for transport models.

Files Modified/Added

• src/NFcore/compartment.hh (New)
• src/NFcore/compartment.cpp (New)
• src/NFcore/molecule.cpp
• src/NFcore/templateMolecule.cpp
• src/NFcore/templateMolecule.hh
• src/NFcore/system.cpp
• src/NFcore/NFcore.hh
• src/NFinput/NFinput.cpp
• src/NFreactions/transformations/transformation.cpp
• src/NFreactions/transformations/transformation.hh
• src/NFreactions/transformations/transformationSet.hh
• src/NFreactions/transformations/moleculeCreator.hh