Refactors VCell Object Cloning and Enhances Libvcell Data Access

[jcschaff]

This update introduces a comprehensive refactoring of object cloning mechanisms within VCell, moving away from generic Java serialization for a more explicit and controlled deep cloning approach.

Key changes include:

• Explicit Deep Cloning: Implements dedicated deepClone() methods for various core objects, including BioNetGen (BNG) specification elements (e.g., BNGMolecule, BNGOutputSpec), geometry surface components (e.g., OrigSurface, Polygons), and math objects (e.g., JumpCondition, AnnotatedFunction).
• Consolidated Cloning via XmlHelper: Centralizes cloning for major VCell documents and components (BioModel, Model, SimulationContext, Geometry, MathDescription, ReactionStep) within XmlHelper, allowing for more robust and controlled replication.
• Libvcell Integration: Configures XmlHelper to utilize XML-based cloning primarily for libvcell contexts, providing a more reliable cloning mechanism for external integrations.
• Symbol Table Management: Ensures that cloned expressions have their symbol table bindings cleared, preventing unintended dependencies and binding issues.
• Improved DataSet Accessibility: Modifies the DataSet class to make its constructor and key methods (read(), getVariableTypeInteger()) public, facilitating direct access and manipulation of field data from libvcell.
• Enhanced Unit System Checks: Adds a new test fault for INCONSISTENT_UNIT_SYSTEM to catch incompatibilities in substance units, improving overall model consistency.

This refactoring aims to improve the stability, performance, and maintainability of object cloning, particularly benefiting integration efforts with libvcell.