🏛️ Architect: Refactor Morphogenesis Stencil Logic

[fderuiter]

This PR refactors the math_explorer/src/biology/morphogenesis.rs file into a modular structure.
It addresses the "God Method" anti-pattern where the finite-difference stencil logic was duplicated between the Euler integrator and the ODE system derivative calculation.

Key Changes:

1. Module Decomposition: Split the monolithic file into kinetics (Reaction Rules), state (Data Structure), and system (Solver Logic).
2. Stencil Abstraction: Created a private, generic apply_reaction_diffusion_stencil method that handles the sliding window optimization and boundary conditions. It accepts a closure to define how the calculated rates are used (state update vs derivative storage).
3. Zero-Cost Abstraction: The closure strategy is inlined, ensuring that the performance matches the original hand-rolled loops (verified via inspection).

This improves maintainability and prepares the module for future extensions (e.g., 2D support) without duplicating the grid iteration logic.

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PR created automatically by Jules for task 1436632298601569212 started by @fderuiter

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[fderuiter]

Run cargo fmt -- --check
Diff in /home/runner/work/math/math/math_explorer/src/biology/morphogenesis/system.rs:1:
-use crate::pure_math::analysis::ode::{OdeSystem, TimeStepper};
use super::kinetics::{ReactionKinetics, SchnakenbergKinetics};
use super::state::TuringState;
+use crate::pure_math::analysis::ode::{OdeSystem, TimeStepper};

/// Represents a 1D Reaction-Diffusion system.
pub struct TuringSystem<K: ReactionKinetics = SchnakenbergKinetics> {
Diff in /home/runner/work/math/math/math_explorer/src/biology/morphogenesis/system.rs:237:
self.d_u,
self.d_v,
self.dx,

•        |i, _u, _v, du, dv| {
  

•            unsafe {
  

•                *out_u.get_unchecked_mut(i) = du;
  

•                *out_v.get_unchecked_mut(i) = dv;
  

•            }
  

•        |i, _u, _v, du, dv| unsafe {
  

•            *out_u.get_unchecked_mut(i) = du;
  

•            *out_v.get_unchecked_mut(i) = dv;
         },
     );
  

  }
  Error: Process completed with exit code 1.

[google-labs-jules]

Run cargo fmt -- --check
Diff in /home/runner/work/math/math/math_explorer/src/biology/morphogenesis/system.rs:1:
-use crate::pure_math::analysis::ode::{OdeSystem, TimeStepper};
use super::kinetics::{ReactionKinetics, SchnakenbergKinetics};
use super::state::TuringState;
+use crate::pure_math::analysis::ode::{OdeSystem, TimeStepper};

/// Represents a 1D Reaction-Diffusion system.
pub struct TuringSystem<K: ReactionKinetics = SchnakenbergKinetics> {
Diff in /home/runner/work/math/math/math_explorer/src/biology/morphogenesis/system.rs:237:
self.d_u,
self.d_v,
self.dx,

•        |i, _u, _v, du, dv| {
  

•            unsafe {
  

•                *out_u.get_unchecked_mut(i) = du;
  

•                *out_v.get_unchecked_mut(i) = dv;
  

•            }
  

•        |i, _u, _v, du, dv| unsafe {
  

•            *out_u.get_unchecked_mut(i) = du;
  

•            *out_v.get_unchecked_mut(i) = dv;
         },
     );
  

  }
  Error: Process completed with exit code 1.

Fixed formatting issues by running cargo fmt.