fix(engine_multiscale): resolved a major species index ordering bug

All jacobian calculations were broken because the indexing used to record the AD tape was broken (see not parallel to) the indexing used by the composition object. A fix for this was to sort the network species by mass. However, more generally we should introduce a mechanism to ensure these two indexed sets always remain parallel

src/include/gridfire/engine/procedures/priming.h

@@ -19,6 +19,7 @@ namespace gridfire {
      *
      * @param netIn Input network data containing initial composition, temperature, and density.
      * @param engine DynamicEngine used to build and evaluate the reaction network.
+     * @param ignoredReactionTypes Types of reactions to ignore during priming (e.g., weak reactions).
      * @pre netIn.composition defines species and their mass fractions; engine is constructed with a valid network.
      * @post engine.networkReactions restored to its initial state; returned report contains primedComposition,
      *       massFractionChanges for each species, success flag, and status code.
@@ -26,7 +27,8 @@ namespace gridfire {
      */
      PrimingReport primeNetwork(
          const NetIn& netIn,
-         DynamicEngine& engine
+         DynamicEngine& engine,
+         const std::optional<std::vector<reaction::ReactionType>>& ignoredReactionTypes
      );
 
     /**
@@ -40,6 +42,7 @@ namespace gridfire {
      * @param composition Current composition providing abundances for all species.
      * @param T9 Temperature in units of 10^9 K.
      * @param rho Density of the medium.
+     * @param reactionTypesToIgnore types of reactions to ignore during calculation.
      * @pre Y.size() matches engine.getNetworkReactions().size() mapping species order.
      * @post Returned rate constant is non-negative.
      * @return Sum of absolute stoichiometry-weighted destruction flows for the species.
@@ -49,7 +52,8 @@ namespace gridfire {
          const fourdst::atomic::Species& species,
          const fourdst::composition::Composition& composition,
          double T9,
-         double rho
+         double rho, const std::optional<std::vector<reaction::ReactionType>> &
+         reactionTypesToIgnore
      );
 
     /**
@@ -63,6 +67,7 @@ namespace gridfire {
      * @param composition Composition object containing current abundances.
      * @param T9 Temperature in units of 10^9 K.
      * @param rho Density of the medium.
+     * @param reactionTypesToIgnore types of reactions to ignore during calculation.
      * @pre Y.size() matches engine.getNetworkReactions().size() mapping species order.
      * @post Returned creation rate is non-negative.
      * @return Sum of stoichiometry-weighted creation flows for the species.
@@ -72,6 +77,6 @@ namespace gridfire {
          const fourdst::atomic::Species& species,
          const fourdst::composition::Composition& composition,
          double T9,
-         double rho
+         double rho, const std::optional<std::vector<reaction::ReactionType>> &reactionTypesToIgnore
      );
  }