WIP: Revamp MassActionJump initialization

[isaacsas]

Immutable MassActionJump Refactor: Move Working Rates to Aggregation Structs

Motivation

MassActionJump.scaled_rates was mutated in-place by update_parameters! (called from remake, reset_aggregated_jumps!, and finalize_parameters_hook!). This caused aliasing bugs where multiple JumpProblems sharing the same MAJ silently corrupted each other's rates, and a class of stale-rate bugs when parameters changed at runtime.

Design

Move the mutable rate working-copy out of MassActionJump into a new maj_rates::Vector{T} field on all aggregation structs. Rate recomputation now happens lazily during initialize! via a new fill_scaled_rates! dispatcher, eliminating update_parameters! entirely.

Key design points:

• Parameterized MAJs (scaled_rates === nothing): fill_scaled_rates! calls maj.param_mapper(dest, maj, params) — the mapper owns all scaling logic
• Non-parameterized MAJs (scaled_rates <: AbstractVector): fill_scaled_rates! copies the immutable scaled_rates into maj_rates
• The JumpProblem constructor no longer eagerly materializes rates — it stores the original {Nothing} MAJ unchanged
• Rates are materialized on every initialize! (triggered by init, solve, or reset_aggregated_jumps!), always reflecting current parameters

Changes

Core infrastructure:

• Add in-place 3-arg mapper callable (mapper)(dest, maj, params) to MassActionJumpParamMapper
• Add fill_scaled_rates! dispatcher that branches on MAJ type parameter
• Update evalrxrate to 4-arg signature (speciesvec, rxidx, majump, maj_rates) taking an explicit rates vector
• Propagate maj_rates through calculate_jump_rate, rejectrx, and get_majump_brackets

Aggregation structs:

• Add maj_rates::Vector{T} field to all 10 aggregation structs (Direct, FRM, DirectCR, SortingDirect, NRM, CCNRM, RSSA, RSSACR, RDirect, Coevolve)
• Add maj_rates::Vector{F} field to spatial RxRates
• Add fill_scaled_rates! call to all initialize! methods and spatial fill_rates_and_get_times!

Problem-level simplifications:

• Remove using_params branch from both JumpProblem constructors (main + PureLeaping) — store original MAJ directly
• Rewrite reset_aggregated_jumps! — remove update_jump_params kwarg (throws informative error if passed)
• Remove update_parameters! calls from remake
• Delete finalize_parameters_hook! entirely
• Remove dead 1-arg mapper callables from MassActionJumpParamMapper

Safety guards:

• Error on merging mapper-backed MAJs (in both massaction_jump_combine and JumpSet vector constructor)
• Error on constructing SpatialMassActionJump from a parameterized MAJ
• rescale_rates_on_update mismatch check on MAJ merges

Tests:

• Update scale_rates_field_test.jl: new tests for mapper callable API, immutability after remake, merge error guards
• Update jprob_symbol_indexing.jl: all rate checks go through discrete_jump_aggregation.maj_rates after init
• Update ssa_callback_test.jl: scale_rates test uses MAJ-level kwarg
• Update regular_jumps.jl: PureLeaping test uses fill_scaled_rates! directly

MTK Compatibility

MTKBase's JumpSysMajParamMapper needs to add one method to integrate with this change:

function (mapper::JumpSysMajParamMapper)(dest::AbstractVector, maj::MassActionJump, params)
    # fill dest with scaled rates from params
    # mapper owns all scaling — check maj.rescale_rates_on_update if needed
end

Dependencies:

SciML/SciMLBase.jl#1252 and SciMLBase release
JumpProcesses #557

[isaacsas]

Pre-merge checklist

Before merging this PR, the following temporary changes need to be reverted:

1. Unpin OrdinaryDiffEqCore — revert =3.15 back to 3.11 in Project.toml
2. Remove SciMLBase branch source — remove the [sources.SciMLBase] section from Project.toml
3. Undo CI workflow changes — remove v10_working from the pull_request.branches trigger in Tests.yml, Downgrade.yml, and ThreadSafety.yml