Document public API coverage gaps

[ChrisRackauckas-Claude]

This PR should be ignored until reviewed by @ChrisRackauckas.

Summary

• Adds docstrings at original definitions where practical for public/exported ModelingToolkit and ModelingToolkitBase API gaps found by the audit.
• Expands several existing docstrings into SciMLStyle-style entries with signatures, arguments, returns, examples, and cross references.
• Adds rendered docs entries for newly documented public API in user API pages and developer-facing structural transformation internals.
• Replaces the @deprecate structural_simplify forms with explicit deprecated wrapper methods so the deprecated API can carry a docstring at its definition point.

Local validation

• Runic.jl passed on all touched Julia files:
  timeout 3600 /home/crackauc/.juliaup/bin/julia +release --startup-file=no -e 'using Pkg; Pkg.activate(; temp=true); Pkg.add("Runic"); using Runic; exit(Runic.main(ARGS))' -- --inplace ...
• Load/precompile check passed:
  timeout 3600 /home/crackauc/.juliaup/bin/julia +release --startup-file=no --project=. -e 'using ModelingToolkitBase, ModelingToolkit; println("loaded ModelingToolkit ", pkgversion(ModelingToolkit))'
• Current local public/exported doc audit after this patch:
  • ModelingToolkit: 16 remaining Docs.hasdoc gaps: @symbolic_wrap, @wrapped, D, DiscreteSystem, ImplicitDiscreteSystem, RuleSet, StructuralTransformations, TimeDomain, UnPack, get_canonical_expr, infimum, is_derivative, istree, solve_for, supremum, t.
  • ModelingToolkitBase: 15 remaining Docs.hasdoc gaps: @symbolic_wrap, @wrapped, D, DiscreteSystem, ImplicitDiscreteSystem, RuleSet, TimeDomain, UnPack, get_canonical_expr, infimum, is_derivative, istree, solve_for, supremum, t.
  • These residuals look like upstream reexports/compat names, generated deprecated aliases, and public-but-not-bound t/D aliases rather than locally owned undocumented definitions.

Blockers / incomplete validation

• Full QA test command timed out after the required 1-hour shell timeout while still running ModelingToolkitBase/test/initializationsystem.jl; no pass is claimed:
  timeout 3600 /home/crackauc/.juliaup/bin/julia +release --startup-file=no --project=. -e 'using Pkg; Pkg.test(; test_args=["QA"])'
• Local docs build with the checkout explicitly developed into the docs environment is blocked by dependency resolution before Documenter runs. The resolver conflict is OptimizationOptimJL 0.4 requiring Optim < 2 while the local stack resolves ForwardDiff 1, restricting Optim to versions that leave no compatible Optim candidate.