Fix NonStiffODE under v7 stack: refresh manifest, fix script bugs, IRKGL16 verbose

Root cause: three independent issues stacked on top of each other.

1. The pinned Manifest had `SymbolicUtils v4.26.0`, which throws
   `Method overwriting is not permitted during Module precompilation`
   in `apply_optimization_rules`. That kills `ParameterizedFunctions`
   precompile, which is the first `using` line in `EnrightPryce_wpd.jmd`
   — so the very first .jmd in the folder crashed at load time on amdci1-1
   (CI run 25374549824, job 75199969438) and the cascading "no such
   directory" errors on the remaining six files were just the runner
   cleanup tripping over the killed job.

2. `enright_pryce.jl` had two latent bugs that newer `SymbolicUtils` /
   `ModelingToolkit` now catch:
   - SF1 equation 2 had `1880 * [y[4] - y[2] * (1 + k)]` (vector literal)
     instead of `1880 * (y[4] - y[2] * (1 + k))`. The bracket made it a
     1-vector, and `SymbolicUtils.AddWorkerBuffer` now throws an
     unequal-shape error when adding scalar/vector symbolic terms.
   - The ND eccentric-orbit family declared `@parameters ε` and threaded
     `[ε => e]` through every `make_ds(...)`, but ε does not appear in
     the equations themselves (the eccentricity enters only via the
     initial conditions). MTK now correctly errors:
     "Expected an `Initial` parameter to exist for variable `ε`, but
     did not find one". Removed the stray parameter.

3. `IRKGL16` (IRKGaussLegendre v1) treats `verbose` as a Bool, but the
   v7 stack passes a `DEVerbosity` struct. Every `WorkPrecisionSet` chunk
   that included `IRKGL16(...)` raised `TypeError: non-boolean ...
   DEVerbosity ... used in boolean context`. Added
   `verbose = SciMLLogging.None()` to those chunks in
   LotkaVolterra/Pleiades/RigidBody/ThreeBody.

4. `OrdinaryDiffEqSIMDRK` (MER5v2/MER6v2/RK6v4) recurses to a
   StackOverflow on `NaNMath.sqrt(::VectorizationBase.Vec{2,Float64})`
   when the RHS calls `sqrt` — which is exactly the ND Kepler family.
   Split out a `setups_nd` without SIMD-RK for the ND section of
   `EnrightPryce_wpd.jmd`. NA/NB/NC don't hit `sqrt` (or skip the one
   problem that does), so SIMD-RK stays in `setups` for them.

Also: `EnrightPryce_wpd.jmd` referenced `NC_PROBLEMS[5]`, but `nc5prob`
is commented out in `enright_pryce.jl` (TODO: MTK v10 N-body). Dropped
the NC5 chunk.

Fix:
- `Pkg.update()` on `benchmarks/NonStiffODE/` (Project.toml unchanged):
  SymbolicUtils 4.26.0 -> 4.30.1, plus the usual transitive bumps
  (ModelingToolkit 11.24 -> 11.26, SciMLBase 3.7 -> 3.13,
   OrdinaryDiffEq* 2.0 -> 2.x.y, LinearSolve 3.75 -> 3.80, etc.).
- Edit `enright_pryce.jl` bracket typo and ε removal.
- Edit `EnrightPryce_wpd.jmd` to drop NC5 and use `setups_nd` for ND.
- Add `verbose = SciMLLogging.None()` to every IRKGL16-containing
  WorkPrecisionSet in Lotka/Pleiades/RigidBody/ThreeBody.

Local verification (julia 1.11.9, --project=benchmarks/NonStiffODE):
- `Pkg.update()` clean; all packages precompile.
- `weave_file(..., (:script,))` succeeds for all 7 .jmd files.
- EnrightPryce smoke run (numruns=3): NA1/2/4/5, NB1/2/3/5, NC1/2/3/4
  pass with full setups (incl. SIMD-RK); ND1-5 pass with setups_nd.
- LotkaVolterra full weave (`(:github,)`) re-run with the IRKGL16
  verbose patch: the previously-erroring chunk now completes.
- Direct IRKGL16 + `verbose=SciMLLogging.None()` WPSet call on
  LotkaVolterra returns clean.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>

Author: ChrisRackauckas

benchmarks/NonStiffODE/EnrightPryce_wpd.jmd

@@ -157,23 +157,27 @@ wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_eve
 plot(wp; title="NC4")
 ```
 
-### NC5
+## Non-Stiff ND Problems
+
+The ND suite uses `sqrt` in the RHS, which triggers a `StackOverflowError` via
+`NaNMath.sqrt(::VectorizationBase.Vec)` when combined with the SIMD-RK stack.
+Use the non-SIMD subset of `setups` for these problems.
 
 ```julia
-prob = NC_PROBLEMS[5]
-test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
-plot(wp; title="NC5")
+setups_nd = [
+    Dict(:alg=>Tsit5()),
+    Dict(:alg=>Vern6()),
+    Dict(:alg=>Vern7()),
+    Dict(:alg=>Vern9())
+]
 ```
 
-## Non-Stiff ND Problems
-
 ### ND1
 
 ```julia
 prob = ND_PROBLEMS[1]
 test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
+wp = WorkPrecisionSet(prob, abstols, reltols, setups_nd; appxsol=test_sol, save_everystep=false, numruns=100)
 plot(wp; title="ND1")
 ```
 
@@ -182,7 +186,7 @@ plot(wp; title="ND1")
 ```julia
 prob = ND_PROBLEMS[2]
 test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
+wp = WorkPrecisionSet(prob, abstols, reltols, setups_nd; appxsol=test_sol, save_everystep=false, numruns=100)
 plot(wp; title="ND2")
 ```
 
@@ -191,7 +195,7 @@ plot(wp; title="ND2")
 ```julia
 prob = ND_PROBLEMS[3]
 test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
+wp = WorkPrecisionSet(prob, abstols, reltols, setups_nd; appxsol=test_sol, save_everystep=false, numruns=100)
 plot(wp; title="ND3")
 ```
 
@@ -200,7 +204,7 @@ plot(wp; title="ND3")
 ```julia
 prob = ND_PROBLEMS[4]
 test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
+wp = WorkPrecisionSet(prob, abstols, reltols, setups_nd; appxsol=test_sol, save_everystep=false, numruns=100)
 plot(wp; title="ND4")
 ```
 
@@ -209,7 +213,7 @@ plot(wp; title="ND4")
 ```julia
 prob = ND_PROBLEMS[5]
 test_sol = solve(prob, Vern9(), abstol=1/10^14, reltol=1/10^14)
-wp = WorkPrecisionSet(prob, abstols, reltols, setups; appxsol=test_sol, save_everystep=false, numruns=100)
+wp = WorkPrecisionSet(prob, abstols, reltols, setups_nd; appxsol=test_sol, save_everystep=false, numruns=100)
 plot(wp; title="ND5")
 ```
 

benchmarks/NonStiffODE/LotkaVolterra_wpd.jmd

@@ -52,7 +52,7 @@ setups = [Dict(:alg=>DP5())
           Dict(:alg=>MER6v2(), :prob_choice => 2)
           Dict(:alg=>RK6v4(), :prob_choice => 2)]
 wp = WorkPrecisionSet(probs, abstols, reltols, setups; appxsol = test_sol,
-    save_everystep = false, maxiters = 10000, numruns = 100)
+    save_everystep = false, verbose = SciMLLogging.None(), maxiters = 10000, numruns = 100)
 plot(wp)
 ```
 
@@ -73,7 +73,7 @@ setups = [Dict(:alg=>DP5())
           Dict(:alg=>Vern6(), :prob_choice => 2)]
 wp = WorkPrecisionSet(
     probs, abstols, reltols, setups; appxsol = test_sol, maxiters = 10000,
-    error_estimate = :L2, dense_errors = true, numruns = 100)
+    error_estimate = :L2, dense_errors = true, verbose = SciMLLogging.None(), numruns = 100)
 plot(wp)
 ```
 
@@ -96,7 +96,7 @@ setups = [Dict(:alg=>DP8())
           Dict(:alg=>Vern8(), :prob_choice => 2)
           Dict(:alg=>Vern9(), :prob_choice => 2)]
 wp = WorkPrecisionSet(probs, abstols, reltols, setups; appxsol = test_sol,
-    save_everystep = false, maxiters = 1000, numruns = 100)
+    save_everystep = false, verbose = SciMLLogging.None(), maxiters = 1000, numruns = 100)
 plot(wp)
 ```
 
@@ -117,7 +117,7 @@ setups = [Dict(:alg=>odex())
           Dict(:alg=>lsoda())
           Dict(:alg=>ARKODE(Sundials.Explicit(), order = 6))]
 wp = WorkPrecisionSet(probs, abstols, reltols, setups; appxsol = test_sol,
-    save_everystep = false, maxiters = 1000, numruns = 100)
+    save_everystep = false, verbose = SciMLLogging.None(), maxiters = 1000, numruns = 100)
 plot(wp)
 ```
 
@@ -137,7 +137,7 @@ setups = [Dict(:alg=>DP8())
           Dict(:alg=>Vern8(), :prob_choice => 2)
           Dict(:alg=>Vern9(), :prob_choice => 2)]
 wp = WorkPrecisionSet(probs, abstols, reltols, setups; appxsol = test_sol, dense = true,
-    maxiters = 1000, error_estimate = :L2, numruns = 100)
+    maxiters = 1000, error_estimate = :L2, verbose = SciMLLogging.None(), numruns = 100)
 plot(wp)
 ```