Fix issues #63 and #65: implement product-side include/exclude filtering and add species observable dirty-flag cache

[akutuva21]

Summary

This PR fixes two open issues in NFsim:

Issue #63 — BNGL rule modifier include_products/exclude_products

The include_products/exclude_products modifiers on BNGL reaction rules were previously unimplemented in NFsim, causing a hard abort at XML load time ("not yet enforced in NFsim"). This PR implements full parsing and enforcement of these modifiers, mirroring the existing include_reactants/exclude_reactants implementation.

Changes:

• Add ProductFilter struct and addExcludeProduct/addIncludeProduct/checkProductFilters methods to TransformationSet
• Parse ListOfExcludeProducts and ListOfIncludeProducts in NFinput.cpp (replaces hard-error abort)
• Check product filters in ReactionClass::fire() after getListOfProducts, treating filter violations as null events

Issue #65 — Species observable performance

SpeciesObservable::isObservable(Complex*) was invoked once per (complex, observable) pair per output sample, resulting in O(C x O x M) cost. For models with many histogram-style Species observables, this caused significant slowdowns. This PR adds a dirty-flag cache on Complex objects to avoid redundant recomputation.

Changes:

• Add _speciesObsCache, _speciesObsCacheSize, _speciesObsDirty to the Complex class
• Cache is invalidated on all complex modification paths (mergeWithList, updateComplexMembership, molecule state changes, bond changes)
• System::outputAllObservableCounts and recalculateAllObservables use the cache to avoid re-walking unchanged complexes for every observable

Testing

• All unit tests pass: util, input, molecule, complex, reactionClass, transformations, templateMolecule, mappingSet
• Build succeeds with zero errors on GCC 13.2.0 / CMake + Ninja

Fixes #63, Fixes #65