feat(Jacobian): Jacobian generation is now stateless.

Previously Jacobians were stored by engines and accessed through engine
accessors (e.g getJacobianMatrixEntry); however, this resulted in
desynced jacobian states. We have changed to a pattern of Engine creates
a jacobian and returns it to the caller. The caller can then do what
they will with it. Because of this the getJacobianMatrixEntry method has
been removed.

BREAKING CHANGE:
    - There is no longer any getJacobianMatrixEntry method on
DynamicEngine classes
    - the generateJacobian method signature has changed to return a
NetworkJacobian object. Internally this uses an Eigen Sparse Matrix to
store its data.

src/include/gridfire/engine/views/engine_multiscale.h

@@ -148,7 +148,7 @@ namespace gridfire {
          * @throws exceptions::StaleEngineError If the QSE cache misses, as it cannot proceed
          *         without a valid partition.
          */
-        void generateJacobianMatrix(
+        [[nodiscard]] NetworkJacobian generateJacobianMatrix(
             const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho
@@ -177,7 +177,7 @@ namespace gridfire {
          *
          * @throws exceptions::StaleEngineError If the QSE cache misses.
          */
-        void generateJacobianMatrix(
+        [[nodiscard]] NetworkJacobian generateJacobianMatrix(
             const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho,
@@ -205,35 +205,13 @@ namespace gridfire {
          *
          * @throws exceptions::StaleEngineError If the QSE cache misses.
          */
-        void generateJacobianMatrix(
+        [[nodiscard]] NetworkJacobian generateJacobianMatrix(
             const fourdst::composition::CompositionAbstract &comp,
             double T9,
             double rho,
             const SparsityPattern &sparsityPattern
         ) const override;
 
-        /**
-         * @brief Gets an entry from the previously generated Jacobian matrix.
-         *
-         * @param rowSpecies Species corresponding to the row index (i_full).
-         * @param colSpecies Species corresponding to the column index (j_full).
-         * @return Value of the Jacobian matrix at (i_full, j_full).
-         *
-         * @par Purpose
-         * To provide Jacobian entries to an implicit solver.
-         *
-         * @par How
-         * This method directly delegates to the base engine's `getJacobianMatrixEntry`.
-         *      It does not currently modify the Jacobian to reflect the QSE algebraic constraints,
-         *      as these are handled by setting `dY/dt = 0` in `calculateRHSAndEnergy`.
-         *
-         * @pre `generateJacobianMatrix()` must have been called for the current state.
-         */
-        [[nodiscard]] double getJacobianMatrixEntry(
-            const fourdst::atomic::Species& rowSpecies,
-            const fourdst::atomic::Species& colSpecies
-        ) const override;
-
         /**
          * @brief Generates the stoichiometry matrix for the network.
          *
@@ -578,6 +556,8 @@ namespace gridfire {
          */
         fourdst::composition::Composition collectComposition(const fourdst::composition::CompositionAbstract &comp, double T9, double rho) const override;
 
+        SpeciesStatus getSpeciesStatus(const fourdst::atomic::Species &species) const override;
+
 
     private:
         /**