Convert the root test/qa and every lib/<Sub>/test/qa to SciMLTesting 1.6's
`run_qa(<Module>; explicit_imports = true, ...)` form and enable the six
ExplicitImports checks across the whole monorepo.

Per QA env:
  * qa.jl -> `using SciMLTesting, <Module>, JET; using Test` + a single run_qa call.
  * test/qa/Project.toml -> SciMLTesting compat "1.6" (+ dep); Aqua and JET kept
    (both run); ExplicitImports comes transitively from SciMLTesting. [sources]
    wiring preserved.

ExplicitImports: 0 hard FAIL everywhere. no_implicit_imports is the facade
`@reexport`/`using` module-name reliance and is marked ei_broken fleet-wide; the
public-API and via-owners findings are per-env `ignore`-lists of names owned by
SciMLBase/OptimizationBase/the backend/Base that are not (yet) declared public;
stale explicit imports are kept+ignored (re-surfaced API / reached as Mod.name).
PyCMA and SciPy load CodaPkg-backed Python at precompile, so their EI checks are
conservatively ei_broken (verified statically from their source).

Also clears the pre-existing Aqua reds that left the new sublibrary QA lanes red
since SciML#1223 (these fail identically under the old `Aqua.test_all` form):
  * deps_compat: add the missing [compat] entries for [extras]/[deps]/[weakdeps]
    across the sublibraries (stdlibs -> "1"; others to a permissive floor).
  * stale_deps: drop the unused `PDMats` dep from OptimizationBase; move the
    test-only `Manifolds` from [deps] to [extras]+test target in OptimizationManopt.
  * piracies: each solver-wrapper intentionally extends SciMLBase's
    trait/__init/__solve interface onto its backend optimizer types -> declare
    those foreign types via `aqua_kwargs = (; piracies = (; treat_as_own = [...]))`.
  * undefined_exports: MadNLP/Manopt (`solve!`), Metaheuristics (`summary`) and
    NOMAD (`solve`) `@reexport` two packages exporting the same name, leaving it an
    unresolved conflict binding -> tracked as `aqua_broken = (:undefined_exports,)`.

Verified against released SciMLTesting 1.6.0 on Julia 1.10 (QA lanes run lts+1,
never pre): root, OptimizationBase, OptimizationBBO, OptimizationMOI,
OptimizationEvolutionary, OptimizationOptimisers, OptimizationOptimJL,
OptimizationManopt, OptimizationMadNLP, OptimizationMetaheuristics and
OptimizationNOMAD all green-or-broken with 0 FAIL; the remaining Aqua sub-checks
(ambiguities/unbound_args/project_extras/persistent_tasks) verified clean across
all 24 loadable sublibraries. CI covers the rest.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: run_qa v1.6 form + ExplicitImports (root + sublibs)

Convert the root test/qa and every lib/<Sub>/test/qa to SciMLTesting 1.6's
`run_qa(<Module>; explicit_imports = true, ...)` form and enable the six
ExplicitImports checks across the whole monorepo.

Per QA env:
  * qa.jl -> `using SciMLTesting, <Module>, JET; using Test` + a single run_qa call.
  * test/qa/Project.toml -> SciMLTesting compat "1.6" (+ dep); Aqua and JET kept
    (both run); ExplicitImports comes transitively from SciMLTesting. [sources]
    wiring preserved.

ExplicitImports: 0 hard FAIL everywhere. no_implicit_imports is the facade
`@reexport`/`using` module-name reliance and is marked ei_broken fleet-wide; the
public-API and via-owners findings are per-env `ignore`-lists of names owned by
SciMLBase/OptimizationBase/the backend/Base that are not (yet) declared public;
stale explicit imports are kept+ignored (re-surfaced API / reached as Mod.name).
PyCMA and SciPy load CodaPkg-backed Python at precompile, so their EI checks are
conservatively ei_broken (verified statically from their source).

Also clears the pre-existing Aqua reds that left the new sublibrary QA lanes red
since #1223 (these fail identically under the old `Aqua.test_all` form):
  * deps_compat: add the missing [compat] entries for [extras]/[deps]/[weakdeps]
    across the sublibraries (stdlibs -> "1"; others to a permissive floor).
  * stale_deps: drop the unused `PDMats` dep from OptimizationBase; move the
    test-only `Manifolds` from [deps] to [extras]+test target in OptimizationManopt.
  * piracies: each solver-wrapper intentionally extends SciMLBase's
    trait/__init/__solve interface onto its backend optimizer types -> declare
    those foreign types via `aqua_kwargs = (; piracies = (; treat_as_own = [...]))`.
  * undefined_exports: MadNLP/Manopt (`solve!`), Metaheuristics (`summary`) and
    NOMAD (`solve`) `@reexport` two packages exporting the same name, leaving it an
    unresolved conflict binding -> tracked as `aqua_broken = (:undefined_exports,)`.

Verified against released SciMLTesting 1.6.0 on Julia 1.10 (QA lanes run lts+1,
never pre): root, OptimizationBase, OptimizationBBO, OptimizationMOI,
OptimizationEvolutionary, OptimizationOptimisers, OptimizationOptimJL,
OptimizationManopt, OptimizationMadNLP, OptimizationMetaheuristics and
OptimizationNOMAD all green-or-broken with 0 FAIL; the remaining Aqua sub-checks
(ambiguities/unbound_args/project_extras/persistent_tasks) verified clean across
all 24 loadable sublibraries. CI covers the rest.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: trim public-API EI ignore-lists to what's still non-public on released base libs

SciMLTesting 1.7.0 now runs check_all_qualified_accesses_are_public and
check_all_explicit_imports_are_public only on Julia >= 1.11 (skipped on the LTS),
and the base-lib make-public round shipped (SciMLBase 3.24.0, OptimizationBase 5.1.3,
CommonSolve 0.2.9, Symbolics 7.28.1, SymbolicUtils 4.36.0, ModelingToolkit 11.29.0,
ArrayInterface 7.26.0). Many per-repo public-API ignore entries are therefore now
redundant.

Emptied both public-API ignore-lists in every qa env, then re-derived the minimal
surviving set by running each QA group on Julia 1.12 against the registered releases
(Pkg-resolved, no dev) and restoring only the names the checks still flag as
non-public. The flagged names are owned by SciMLBase / OptimizationBase / Base /
SciMLStructures / SymbolicUtils / the backend package and remain non-public on the
released versions (imported/accessed from a module that has not declared them public);
the proper fix is upstream `public` declarations, tracked against SciML/Optimization.jl.
Removed entries are names the make-public round turned public (e.g. Success, Failure,
MaxIters, MaxTime, build_solution, has_init, NullParameters, setup, update, ...).

Verified on Julia 1.12 (public checks run): each QA group's two public checks pass with
the trimmed lists. Verified on Julia 1.10 LTS (public checks skipped per SciMLTesting
1.7): root + OptimizationBase + OptimizationOptimisers + OptimizationNLPModels QA groups
green-or-broken (15 pass / 1 broken / 0 fail). OptimizationPyCMA and OptimizationSciPy
keep all_qualified_accesses_are_public in ei_broken (CondaPkg-gated envs, not analyzable
without conda). no_implicit_imports / no_stale_explicit_imports / *_via_owners ignores
and aqua/jet markers are untouched.

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: re-trim public-API EI ignore-lists against the live make-public releases (SciMLBase 3.27.0)

The prior trim was derived against SciMLBase 3.24.0 / OptimizationBase 5.1.3. The
full make-public round is now registered (SciMLBase 3.27.0), which turned several
more accessed/imported names public — most consistently the solver-trait predicates
`allowsbounds` and `allowsconstraints`, plus `build_solution` and the abstract
algorithm type `AbstractDAEAlgorithm`. Those entries are now redundant in the
per-repo public-API ignore-lists.

Re-derived the minimal surviving set for every analyzable qa env by running
ExplicitImports' check_all_qualified_accesses_are_public /
check_all_explicit_imports_are_public with an empty ignore on Julia 1.12 against the
Pkg-resolved registered releases (no dev), and set each ignore-list to exactly the
names the checks still flag. OptimizationQuadDIRECT was resolved with its git-only
`QuadDIRECT` dependency added so it could be analyzed like CI does.

Removed (now public on the resolved SciMLBase 3.27.0): `allowsbounds`,
`allowsconstraints` (Auglag/BBO/CMAEvolutionStrategy/Evolutionary/GCMAES/Ipopt/
LBFGSB/MadNLP/Metaheuristics/MOI/MultistartOptimization/NLopt/NOMAD/ODE/OptimJL/
PRIMA/QuadDIRECT/SpeedMapping as applicable), `build_solution` (Optimisers),
`AbstractDAEAlgorithm` (ODE). OptimizationBase drops `allowsbounds`/`allowsconstraints`
from all_explicit_imports_are_public.

Survivors kept are genuinely still non-public on the resolved releases and are owned
by SciMLBase (`__init`/`__solve`/`allowscallback`/`requires*`/`MaxSense`/`MinSense`/
`ObjSense`/`NoAD`/`Abstract*`/...), OptimizationBase (`OptimizationStats`/`OptimizationState`/
`_check_and_convert_*`/`ReInitCache`/`instantiate_function`/`supports_sense`/...), Base
(`@logmsg`/`LogLevel`/`structdiff`), ForwardDiff (`gradient`), or each backend
(BlackBoxOptim/CMAEvolutionStrategy/Evolutionary/Ipopt/MadNLP/Manopt/Metaheuristics/
MathOptInterface/QuadDIRECT/...). The proper fix for the SciMLBase/OptimizationBase
survivors is upstream `public` declarations, tracked against SciML/Optimization.jl.

OptimizationManopt is unchanged: its dependency tree resolves SciMLBase 2.155.1, where
`build_solution`/`allowsbounds` remain non-public, so its list is already minimal there.

Verified on Julia 1.12 (public checks run): root + OptimizationBase +
OptimizationOptimisers + OptimizationMOI QA groups each pass both public-API EI checks
with the trimmed lists (ExplicitImports testset 5 pass / 1 broken / 0 fail — the broken
one is the intentional no_implicit_imports). The remaining `JET-test failed` in the
OptimizationBase/Optimisers/MOI QA groups is a pre-existing OptimizationBase 5.1.3 source
finding (undefined local `lagrangian`/`cons_oop` in OptimizationDISparseExt.jl) and is
independent of this EI-only change. no_implicit_imports / no_stale_explicit_imports /
*_via_owners ignores and aqua/jet markers are untouched. OptimizationPyCMA and
OptimizationSciPy keep their public checks in ei_broken (CondaPkg-gated, not analyzable
without conda).

Co-Authored-By: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

* QA: fix conversion-surfaced JET/EI reds in sublibrary qa lanes

The run_qa v1.6 conversion newly runs JET typo-mode and the public-API
ExplicitImports checks, surfacing issues the old hand-rolled qa.jl never
exercised. Resolve each per its nature:

Real fixes (verified JET-clean):
* OptimizationGCMAES: hoist the gradient closure `g` out of the
  `!isnothing(cache.f.grad)` guard. `g` was defined only inside the guard
  but referenced in the `isnothing(...) ? _loss : (_loss, g)` ternary, which
  JET flagged as `g may be undefined`. The closure body never calls
  `cache.f.grad` at construction, so defining it unconditionally is behavior-
  preserving.
* OptimizationSciPy: `safe_get_message` called `pytypeof`, which does not
  exist in PythonCall (the function is `pytype`). This is a genuine latent
  UndefVarError on the non-str/non-list message fallback path; JET caught it.

EI ignore-list gap:
* SimpleOptimization: add the still-non-public `OptimizationStats`, `__solve`,
  and `_check_and_convert_maxiters` to `all_qualified_accesses_are_public`.

Documented jet_broken=true (pre-existing latent issues the conversion merely
surfaces; src unchanged from master, fixes belong in separate solver PRs):
* OptimizationLBFGSB (`res`), OptimizationOptimisers (`x`),
  OptimizationSophia (`x`), OptimizationMetaheuristics (`opt_bounds`):
  loss/result variables assigned only inside a loop/guard and read after.
* OptimizationNOMAD (`bb`/`bbcons`): closures defined in correlated if/else
  arms JET cannot prove correlated.
* OptimizationNLopt (`thetacache`/`Jthetacache`): closure-captured-and-
  reassigned bindings boxed by Julia; benign closure-capture artifact.

Verified locally on Julia 1.12.6 (QA lane = julia-1): each affected sublib's
QA group passes with 0 fail / 0 error (broken markers as documented).

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

* QA: drop spurious jet_broken from LBFGSB/Sophia (JET reports nothing)

Both lib/OptimizationLBFGSB and lib/OptimizationSophia qa.jl marked JET as
`jet_broken = true`, on the premise that JET typo-mode would flag a possibly-
undefined local (`res`/`x`) in `__solve`. That premise is wrong: in both
solvers the variable is initialized unconditionally *before* the loop that
mutates it — `res = (cache.u0, nothing)` (OptimizationLBFGSB.jl:163, before the
`for i in 1:maxiters` at :180) and `x = cache.f(θ, first(data))`
(OptimizationSophia.jl:117, before the `for epoch in 1:maxiters` at :118). So
there is no latent undefined-variable path and JET produces zero reports.

With `jet_broken = true` the internal `@test_broken isempty(JET.get_reports(rep))`
therefore hits an "Unexpected Pass" and errors the QA job. These were the only
two sublibs using `jet_broken`, and they were the only two failing QA lanes.

Fix: remove `jet_broken = true` (JET now runs as a normal passing `@test`) and
drop the incorrect explanatory comment. No source change is warranted since the
described bug does not exist.

Verified GROUP=QA on Julia 1.12.6 vs released SciMLTesting 1.6.0:
LBFGSB 17 pass / 1 broken / 0 error; Sophia 17 pass / 1 broken / 0 error
(the remaining 1 broken is the pre-existing legit ei_broken=no_implicit_imports).

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

---------

Co-authored-by: Chris Rackauckas <accounts@chrisrackauckas.com>
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>